Release Announcements

• Entrez-style search box. Our site search now automatically queries multiple domains and allows one click access to search results across VectorBase data.
• New gene sets. Aedes, Culex and Ixodes gene sets have all been updated with community-supplied gene improvements.
• Updated genome browser. VectorBase now runs e! version 66.

• The guide provides the list of resistant, susceptible and humanized mouse models used in the infection studies.
• Pathogens (bacteria, eukaryotic pathogens and viruses) are linked out directly to their corresponding BRC websites (PATRIC, EuPathDB, ViPR and IRD).
• Mouse strains selected for the pathogen infection studies are linked out to the JAX mice database for detailed mouse strain information and purchasing information (if any).
• The PubMed and Mouse Genome Informatics (MGI) references are provided.

• Improved search functionality. You can now search the expression data, population data and ontologies from the same search box.
• Simplified, enhanced new graphical interface to our expression maps.
• You can associate publications to genes from within the genome browser via the PubMed link in the left hand menu of a gene page

• T. brucei protein palmitoylation data (Emmer et. al.).

• To search this data, go to the "Identify Genes based on Mass Spec. Evidence" and select "Procyclic form palmitoylated proteins (Emmer et al.)" under Trypanosoma brucei.  This search will return all genes that have mass spec palmitoylation evidence.
  

• Mass spec data can also be visualized in the protein section of gene pages (for example, scroll down to the "Protein" section of this gene page) and in the genome browser.  Mousing over peptide graphics displays additional peptide and modification site information.   

• Single nucleotide polymorphism (SNP) calls based on high throughput sequencing data of T. brucei 927 and 427 provided by George Cross.  Genes with SNPs can be identified based on their type (synonymous, nonsynonymous, etc.), their frequency and/or their depth of coverage. 
  

• To search this data click on "Identify Genes based on HTS SNP Characteristics" under the heading "Population Biology".
  

• SNP data is represented as a table on gene pages. For example, if you visit the gene page for Tb927.1.1740, you can view a table under the heading "SNPs summary" which includes information about the SNPs found in this gene based on this comparison.

• An additional view of SNPs is available in the genome browser where SNPs can be visualized based on their coding potential (represented as colored diamonds).  Mousing over the diamonds reveals a popup with additional information about the SNP at that specific location.  Also, the mouse over includes a link to the SNP record page with additional information. 
  

• The actual sequence reads in a particular region can be visualized in gbrowse by turning on the "Sequence Reads" track under the heading "High Throughput Sequencing (HTS) SNPs".
  

• Transcriptome-wide mRNA degradation data for T. brucei (Manful et. al.).  This data is represented on gene pages in graphical (fold change and percentile) and tabular (raw data) formats.  To see this data visit any T. brucei gene page (for example Tb927.8.620) and scroll down to the section called "T. brucei RNA Sequence of transcriptome-wide mRNA degradation" under "Expression".

• Leishmania tarentolae Parrot-TarII genome sequence and annotation (Raymond et. al.).  Chromosome sequence and annotations for Leishmania tarentolae are provided by the CIHR Group on host pathogen interactions (Marc Ouellette, Jacques Corbeil, Barbara Papadopoulou, Michel J. Tremblay, Fr�d�ric Raymond, S�bastien Boisvert from Universit� Laval, and Martin Olivier from McGill University).

• Genes may be queried based on gene IDs, text terms, EC numbers, GO terms, sequence features (length, introns, signal sequences, Pfam domains), etc.
• Genes and sequences may also be interrogated based on BLAST similarity, user-defined motifs, etc.
• Gene pages and synteny data are also available.
  

• Draft assemblies of the genome sequences from the Trypanosomatid sequencing white paper.  This data is graciously provided prepublication and full credit and data usage information is available by clicking on the sequence name:
  

• Endotrypanum monterogeii strain LV88

• Leishmania major strain LV39c5
  

• Leishmania panamensis strain L13

• Genomic sequence data is available under the heading "Genomic Sequences" on the home page and may be searched by species, genomic sequence IDs and BLAST.
  

• Additionally, genomic sequence data may be downloaded from the TriTrypDB download directory.

• New Gene IDs -- T. cruzi IDs have been truncated by GeneDB to make them more user friendly.  Old IDs have been mapped to the new ones (ie. you can search with either old or new IDs).  Currently the old ID is displayed with the new gene ID on gene pages (old ID/new ID).  In a future release the only the new IDs will be displayed at the top of the page.
  

• The genome browser has been updated.  This newer version includes several improvements and functionalities.  A tutorial highlighting some of the new features is also available.  

• A new column analysis tool is now available that allows you to generate a word cloud or histogram based on the data in result columns.  To access this feature, run any search that returns a list of results then click on the icon next to the product description column name.  This will reveal a popup with the option to select "Word Cloud".  Look for this analysis feature to be activated on additional columns in future releases.

• Several new tutorials have been generated:

• The genome browser.
• Customizing restriction sites in the genome browser.
• Identifying isolates based on geographic location.
• Dealing with invalid IDs and search strategies.
• Using the orthology phylogenetic profile search.

• Strand-specific RNA-sequence data from T. gondii ME49 oocyst stages provided prepublication by the John Boothroyd and Brian Gregory groups.  These data are available as genome browser tracks. 
  

• Note:  RNA-sequence data is also used to visualize intron/exon boundaries (based on intron-spanning reads).  Data specific or unified splice junction tracks can be visualized in the genome browser.

• Microarray data from wild type and several bradyzoite differentiation mutants of T. gondii type I RH strain (Lescault et. al., 2010, PLoS One).  Microarray data can be searched in the transcript expression section of ToxoDB.  Searching this data allows you to identify differences between wild type and mutant parasites as well as genes that are differentially regulated during a bradyzoite differentiation time course.  Here is a search strategy that identifies genes that are upregulated during the differentiation series.  In addition, microarray data is displayed on gene pages in the expression section where data can be viewed as fold change differences, percentile or in tabular format.  

• The genome browser has been updated.  This newer version includes several improvements and functionalities.  A tutorial highlighting some of the new features is also available.  

• A new column analysis tool is now available that allows you to generate a word cloud or histogram based on the data in result columns.  To access this feature, run any search that returns a list of results then click on the icon next to the product description column name.  This will reveal a popup with the option to select "Word Cloud".  Look for this analysis feature to be activated on additional columns in future releases.

• Several new tutorials have been generated:

• The genome browser.
• Customizing restriction sites in the genome browser.
• Identifying isolates based on geographic location.
• Dealing with invalid IDs and search strategies.
• Using the orthology phylogenetic profile search.

• The genome browser has been updated.  This newer version includes several improvements and functionalities.  A tutorial highlighting some of the new features is also available.  

• A new column analysis tool is now available that allows you to generate a word cloud or histogram based on the data in result columns.  To access this feature, run any search that returns a list of results then click on the icon next to the product description column name.  This will reveal a popup with the option to select "Word Cloud".  Look for this analysis feature to be activated on additional columns in future releases.

• Several new tutorials have been generated:

• The genome browser.
• Customizing restriction sites in the genome browser.
• Identifying isolates based on geographic location.
• Dealing with invalid IDs and search strategies.
• Using the orthology phylogenetic profile search.

• The genome browser has been updated.  This newer version includes several improvements and functionalities.  A tutorial highlighting some of the new features is also available.  

• A new column analysis tool is now available that allows you to generate a word cloud or histogram based on the data in result columns.  To access this feature, run any search that returns a list of results then click on the icon next to the product description column name.  This will reveal a popup with the option to select "Word Cloud".  Look for this analysis feature to be activated on additional columns in future releases.

• Several new tutorials have been generated:

• The genome browser.
• Customizing restriction sites in the genome browser.
• Identifying isolates based on geographic location.
• Dealing with invalid IDs and search strategies.
• Using the orthology phylogenetic profile search.

• P. vivax Schizont stage proteome from human blood samples (Roobsoong et. al.).  This data can be searched by choosing "Schizont stage proteome from human blood sample (Roobsoong et al.)" in the P. vivax section of the Mass Spec. Evidence search page. In addition, peptide evidence is displayed on gene pages in the Protein Section and in the genome browser by turning on the track specific for this data.  This search strategy identifies all P. vivax genes with mass spec evidence from this study.

• P. falciparum nuclear and cytosolic fractions from rings, trophozoites, and schizonts graciously provided prepublication by Till Voss and colleagues.  This data can be searched by choosing "P. falciparum cytoplasmic and nuclear fractions from rings, trophozoites and schizonts (3D7) (Oehring and Woodcroft et al. - unpublished)" in the P. falciparum section of the Mass spec. evidence search page. In addition, peptide evidence is displayed on gene pages in the Protein Section and in the genome browser by turning on the track specific for this data.  This search strategy identifies all P. falciparum genes with mass spec evidence from this study. 

• P. falciparum blood stage phosphoproteome (Treeck & Sanders et. al.).  This data can be searched by choosing "Blood stage phosphoproteome and total proteome (3D7) (Treeck & Sanders et al.)" in the P. falciparum section of the Mass spec. evidence search page. In addition, peptide evidence is displayed on gene pages in the Protein Section and in the genome browser by turning on the track specific for this data.  This search strategy identifies all P. falciparum genes with phospho mass spec evidence from this study.

• P. falciparum ChIP-sequence data from the histone variant H2Bv (three time points) and  CenH3 (schizonts) represented as coverage plots in the genome browser.  This data was graciously provided prepublication by the Stunnenberg group.

• Genome-wide expression level polymorphisms (ELPs) from a genetic cross between phenotypically distinct parasite clones of P. falciparum (HB3 and Dd2) (Gonzales et. al.). This data may be searched and visualized in many ways:

• Genes may be identified based on their association to genomic segments, expression profile similarity or similarity of genetic association.  These searches are based on the microarray expression profiles generated in each of the progeny and can be accessed in the microarray search page under the heading "eQTL studies on Hb3 X Dd2 progeny (Ferdig)". 

• Genomic segments can be identified based on their association to genes.  This search is available by clicking on "P.f. eQTL HB3-Dd2 cross (segments by association to genes)" under the heading "Genomic Segments" in the "Identify other data types" section of the PlasmoDB home page.
  

• Regions/spans that are associated by eQTL are displayed in a table on gene pages (example gene page). The table "Regions/Spans associated by eQTL experiment on HB3 x DD2 progeny" includes a column for haplotype blocks associated the gene, the coordinates of the haplotype block, LOD scores, and links to searches for genes contained within the region or associated with the region.

• Both microsatellites and haplotype blocks are available as tracks in the genome browser. 
  

• Improved linking to the Rodent Malaria Genetically Modified (RMgm) parasites database.  A dedicated "Phenotype" table is now available on gene pages with information about the genetic modification and linkouts to PubMed and the RMgm database.  As an example, you can scroll down and expand the table under the heading "Phenotype" on the  gene page for a putative P. berghei guanylyl cyclase.
  

• Updated linkouts to the Malaria Parasite Metabolic Pathways (MPMP) database.  Numerous pathways have been added and updated by Dr. Hagai Ginsburg.   Genes included in the MPMP database can be searched based on metabolic pathway in PlasmoDB here.

• New Gene IDs -- Please read the news item from GeneDB regarding assignment of new P. falciparum gene IDs. We will be updating to these new IDs in the next release. Rest assured that both PlasmoDB and GeneDB will proper mapping of old IDs to the new ones (in other words, you will always be able to search with the old or new IDs). Currently in PlasmoDB we are displaying the new Gene ID next to the old one at the top of gene pages (old ID/new ID).     

• The genome browser has been updated.  This newer version includes several improvements and functionalities.  A tutorial highlighting some of the new features is also available.  

• A new column analysis tool is now available that allows you to generate a word cloud or histogram based on the data in result columns.  To access this feature, run any search that returns a list of results then click on the icon next to the product description column name.  This will reveal a popup with the option to select "Word Cloud".  Look for this analysis feature to be activated on additional columns in future releases.

• Several new tutorials have been generated:

• The genome browser.
• Customizing restriction sites in the genome browser.
• Identifying isolates based on geographic location.
• Dealing with invalid IDs and search strategies.
• Using the orthology phylogenetic profile search.

• The genome browser has been updated.  This newer version includes several improvements and functionalities.  A tutorial highlighting some of the new features is also available.  

• A new column analysis tool is now available that allows you to generate a word cloud or histogram based on the data in result columns.  To access this feature, run any search that returns a list of results then click on the icon next to the product description column name.  This will reveal a popup with the option to select "Word Cloud".  Look for this analysis feature to be activated on additional columns in future releases.

• Several new tutorials have been generated:

• The genome browser.
• Customizing restriction sites in the genome browser.
• Identifying isolates based on geographic location.
• Dealing with invalid IDs and search strategies.
• Using the orthology phylogenetic profile search.

• Proteomic data from day 10 mature T. gondii M4 strain (type II) oocysts.  These data were graciously provided prepublication (Heather M. Fritz, Paul W. Bowyer, Matthew Bogyo, Patricia A. Conrad, John C. Boothroyd).   Three oocyst fractions were generated and examined by mass spec (additional experimental details are available in the data sources section).  

• Genes with mass spec evidence from each of these fractions may be interrogated in ToxoDB.  For example, this search strategy identifies genes that have mass spec evidence from the outer wall fraction (not treated) that do not have proteomics expression evidence from the inner wall (bleach treated) fraction.  This search can be further refined to ask how many of these genes also contain predicted transmembrane domains.
  

• Phosphoproteomic and total proteomic data from intracellular and extracellular T. gondii RH strain.  This data was graciously provided prepublication and is now in press (Treeck et. al., 2011, Cell Host & Microbe).  Additional experimental details are available in the data sources section.  

• This search strategy identifies Toxoplasma (GT1 and ME49 genes) genes with evidence of phosphorylation during the intracellular stage that do not have evidence of phosphorylation in purified extracellular parasites.

• Calcium-dependent phosphoproteomic data from intracellular T. gondii RH strain.  This data was graciously provided prepublication and is now in press (Nebl et. al., 2011, PLoS Pathogens).  

• This search strategy identifies genes that have evidence of calcium-dependent phosphorylation based on SEQUEST and MASCOT analysis.

• Note: all proteomic data can be viewed graphically on gene pages or the genome browser in ToxoDB.  In addition, moving your cursor over peptide graphics displays additional information including the peptide sequence and phosphorylation sites when available.  For example, you can view peptide evidence from all the above described data in the "protein features" section on this gene page. Also, all protein expression data in ToxoDB can be searched in the "Protein expression" section.  

• Microarray data from TgGCN5-A knockout T. gondii type I RH strain parasites (Naguleswaran et. al., 2010, PLoS Pathogens).  Microarray data can be searched in the transcript expression section of ToxoDB.  Here is an search strategy that identifies genes that are upregulated in wild type parasites under stress conditions and not upregulated in GCN5 knockout parasites under the same conditions.

• Microarray data from T. gondii parasites soon after invasion (Gaji et. al., 2010, Molecular Microbiology).  Microarray data can be searched in the transcript expression section of ToxoDB.  Here is a search strategy that identifies genes that are differentially regulated between extracellular and intracellular parasites.  

• Single nucleotide polymorphism (SNP) data based on comparisons of the T. gondii RH strain (This data was graciously provided prepublication by Marc-Jan Gubbles).  Using this data, genes in ToxoDB may be identified based on their high throughput sequencing (HTS) SNP characteristics (comparing RH to GT1 and ME49).   On the SNP search page (under the heading "Population Biology"), selecting "HTS SNP characteristics" allows you to define the type of SNPs you are interested in. 
  

• This search identifies all genes in ME49 that contain 20 or more nonsynonymous SNPs compared to RH.  
• HTS SNPs are summarized on gene pages in the "SNPs Summary" table.
• SNP records can also be searched using the SNP search tools under the heading "Identify other data types".  Searches include identifying SNPs based on ID, genomic location or GeneID.  These searches return SNP records which are populated with additional information such as sequence surrounding a SNP.
  
• In addition, an alignment pileup of reads around a specific SNP can be viewed to assess the quality of the SNP call.
  

• The unannotated genome sequence T. gondii strains CatBR9 and the early diverging apicomplexan Gregarina niphandrodes provided by the Toxoplasma white paper sequencing project are now available.  This data can be searched from the  "Genomic Sequences" section under the heading "Identify other data types" on the home page.  Genome sequences from this effort will be incorporated into ToxoDB release as they become available.  A webpage with updated information on the status of sequencing is maintained by Hernan Lorenzi at the J. Craig Venter Institute.  In addition, a PDF of the sequencing white paper is available for download.

• A new column analysis tool is now available that allows you to generate a word cloud or histogram based on the data in result columns.  To access this feature, run any search that returns a list of results then click on the icon next to the product description column name.  This will reveal a popup with the option to select "Word Cloud".  Look for this analysis feature to be activated on additional columns in future releases.

• First announcement of the new population biology resource prototype web interface
• Updated Ensembl genome browser (to schema 63)

• E. histolytica Rahman and moshkovskii genome sequence is now available in AmoebaDB.  This data was graciously provided prepublication by Gareth Weedall and Neil Hall (Institute of Integrative Biology, University of Liverpool, UK). Genomic sequence data from unannotated genomes can be searched from the "Genomic Sequences" section under the heading "Identify other data types" on the home page. Sequence data may be searched based on ID, organism or BLAST.

• T. brucei RNA sequencing Data (Archer et. al.)

• To search this data, go to the "Identify Genes based on RNA Seq Evidence" and select either fold change (with or without P value) or percentile searches under the heading "Cell Cycle (Archer)".

• Graphs and tables representing the expression and percentile values for individual genes are available in the "Expression" section of gene pages.

• Genome browser tracks are available that show RNA-seq coverage plots throughout the cell cycle. 
  

• T. cruzi comparative genomic hybridization of 16 strains (Minning et. al.).

• This data is available as a genome browse track.  Amplifications are indicated as positive values on the graph while deletions are indicated as negative values.  A link showing this data on the entire chromosome 37 of T. cruzi can be accessed here.

• Sequence and annotation of the P. falciparum IT strain produced by the Parasite Genomics Group at the Wellcome Trust Sanger Institute with funding from the EVIMalaR Consortium (a European Commission Funded Network of Excellence).  While this data has been graciously provided prepublication to the community its usage for large scale genomic analysis is bound by a data usage policy.

• Updated linkouts to the Malaria Parasite Metabolic Pathways (MPMP) database.  Numerous pathways have been added and updated by Dr. Hagai Ginsburg.   A full description of new pathways is available here and genes included in the MPMP database can be searched based on metabolic pathway in PlasmoDB here.

• You can now view intron/exon boundaries based on available RNA sequence data.  boundary determination was performed using the RNA-Seq Unified Mapper (RUM). To view intron/exon boundary calls, turn on the "RNA-seq alignments RUM Intron" track in the genome browser.  Here is a link to a gene that is predicted to have multiple splice variants based on the annotation provided by GeneDB with the RUM intron tracks turned on.  To get additional information mouse over the tracks and/or the track names.

• Strand-specific RNA sequence and non coding RNA (ncRNA) data for T. gondii and N. caninum (graciously provided prepublication by Brian Gregory, University of Pennsylvania).  This data was generated as part of one of the funded driving biological projects.
  


• An example region of the Toxoplasma genome with RNA sequence coverage-plot tracks turned on can be accessed here (note: experiment was performed using VEG parasites and was mapped to both VEG and ME49 sequence in ToxoDB).   This data is represented in two tracks:  

•  "T.gondii VEG mRNA RNAseq - Unique Aligners - (log2 Coverage) (Gregory)" which includes strand-specific coverage plots (Blue for the forward strand and red for the reverse strand).

• "T.gondii VEG mRNA RNAseq - Nonunique Aligners - (log2 Coverage) (Gregory)" which shows coverage plots for regions where probes did not uniquely align (ie. gives and indication of possible repetitive regions).

• An example region of the Toxoplasma genome with ncRNA sequence coverage-plot tracks turned on can be accessed here (note: experiment was performed using RH and ME49 parasites and was mapped to ME49 sequence in ToxoDB.  RH data was also mapped against the GT1 strain).

• New T. gondii ME49 cosmid end library mapping to the genome are now available in the genome browser.  The libraries were generated in Laura Knolls laboratory, University of Wisconsin.

• Updated restriction fragment polymorphism (RFLP) data provided by Chunlei Su, University of Tennessee.  RFLP data may be searched based on Genotype or  Genotype Number.

• The unannotated genome sequence T. gondii strains FOU provided by the Toxoplasma white paper sequencing project is now available.  This data can be searched from the  "Genomic Sequences" section under the heading "Identify other data types" on the home page.  Genome sequences from this effort will be incorporated into ToxoDB release as they become available.  The latest updated information on the status of sequencing is available here.  The sequencing white paper is available here.

• Genome sequence and annotation of Eimeria tenella graciously provided prepublication by Adam Reid and colleagues (Parasite Genomics group at the Wellcome Trust Sanger Institute, UK).  Annotated genomes may be investigated in ToxoDB using multiple searches for example, genes may be identified based on text, ID, BLAST, GO terms, presence of transmembrane domains or signal peptides, orthology, etc.  Here is a search strategy that identifies all E. tenella genes predicted to contain a secretory signal peptide and are possible kinases (note: the orthology step at the end allows identification of possible gene families):

• You can now view intron/exon boundaries based on available RNA sequence data.  boundary determination was performed using the RNA-Seq Unified Mapper (RUM). To view intron/exon boundary calls, turn on the "RNA-seq alignments RUM Intron" track in the genome browser.  Here is a link to a gene that may require reevaluation based on RUM intron analysis.  To get additional information mouse over the tracks and/or the track names.

• Whole genome shotgun sequence of the following species generated by The Broad Institute Genome Sequencing Platform with Federal funds from the National Institute of Allergy and Infectious Diseases under Contract No.: HHSN2722009000018C:

• Encephalitozoon cuniculi EcI
• Encephalitozoon cuniculi EcII
• Encephalitozoon cuniculi EcIII
• Nematocida parisii ERTm1
  
• Nematocida parisii ERTm2
• Vavraia culicis floridensis 
• Vittaforma corneae
  

• Genomic sequence data from unannotated genomes can be searched from the "Genomic Sequences" section under the heading "Identify other data types" on the home page. Sequence data may be searched based on ID, organism or BLAST.

• Sequence and annotation for Encephalitozoon hellem (graciously provided prepublication by Patrick Keeling's group).

• Annotated genomes can be searched using any of the searches under the heading "Identify Genes by:" on the MicrosporidiaDB home page.  Searches include, identifying genes by text, ID, BLAST, GO terms, presence of transmembrane domains or signal peptides, orthology, etc.  Here is a search that identifies all E. hellem genes that have at least 7 transmembrane domains and do not have orthologs in mammals:

• Sequence and annotation for Nosema ceranae BRL01 obtained from GenBank and published by Cornman et. al.

• Here is a search that quickly defines  E. hellem orthologs of  N. ceranae genes (note the column labeled as "Input orthologs" refers to the N. ceranae genes in the same orthology group as the E. hellem "Gene" in the first column):

• Pre-site for Glossina moritans. Features mapped to the genome and preliminary gene sets available.
• New microarray data from Christian et al. and Cassone et al.

• E. histolytica glycoproteins proteomics data from Carpentieri et. al.  To search this data click on the protein expression link under the "Identify Genes by:" heading, then click on "Mass Spec. Evidence".  On this page you can expand the "Entamoeba histolytica" item and select your data "Mass Spec/Glycosylation" and click "Get Answer". 

• As usual you can combine search results with other searches in a strategy.  Here is an example search strategy that leverages orthology to identify all Entamoeba orthologs of E. histolytica genes with proteomics evidence from this data, that are predicted to have a predicted signal peptide.

• T. brucei RNA sequencing spliced leader expression data (Nilsson et. al.).

• To search this data, go to the "Identify Genes based on RNA Seq Evidence" and select either fold change or percentile searches under the heading "Splice Sites (Nilsson)".

• Graphs and tables representing the expression and percentile values for individual genes are available in the "Expression" section of gene pages.

• Genome browser tracks are available that show splice site locations.

• T. brucei high-throughput phenotyping of bloodstream and procyclic form parasites (Alsford et. al.).

• To search this data click on "Putative Function" under the heading "Identify Genes by" on the home page then click on "High-Throughput Phenotyping".  A sample strategy that searches this data for genes that are likely essential in all stages or time points examined can be accessed here. 
  

• Graphs and tables representing the expression and percentile values for individual genes are available in the "Phenotype" section of gene pages.

• Genome browser tracks of coverage plots for each sample from this experiment are available.

• T. brucei microarray data based on induced DHH1 RNA helicase in wild type and DEAD:DQAD mutant procyclic trypanosomes (Kramer et. al.).

• To search this data, go to the "Identify Genes by Microarray Evidence section"and click on either the fold change or percentile searches under the heading "RNA helicase DHH1 and post transcriptional regulation (Carrington)".

• Graphs and tables representing the expression and percentile values for individual genes are available in the "Expression" section of gene pages.

• T. brucei microarray data based on heat shock treated and control procyclic trypanosomes (Kramer et. al.).

• To search this data, go to the "Identify Genes by Microarray Evidence section"and click on either the fold change or percentile searches under the heading "Heat shock and post transcriptional regulation (Carrington)".

• Graphs and tables representing the expression and percentile values for individual genes are available in the "Expression" section of gene pages.

• L. major and L. infantum RNA sequence data highlighting splice leader and polyA sites are available as genome browser tracks.  This data was graciously made available prepublication by Dr. Peter Myler's group at Seattle BioMed.

• L. mexicana amastigote proteomics data (Paape et. al.).

• This data can be searched by going to the "Protein Expression" section under the heading "Identify Genes by" on the home page, then selecting the "L. mexicana intracellular Gel free analysis" option.  As usual results from any search can be combined with other searches in TriTrypDB.  For example, here is a search strategy that identifies genes with proteomics evidence from this data that have a predicted signal peptide.

• Proteomics data may also be viewed on gene pages as tables and graphical representation (scroll down to the "Protein Expression" section) or in the genome browser by selecting the appropriate track(s) and updating the image.  Here is a link to a genome browser section highlighting this proteomics data.

• T. cruzi Sylvio X10/1 genome sequence data (Franzen et. al.). 
  

• Draft assemblies of the genome sequences from the Trypanosomatid sequencing white paper.  This data is graciously provided prepublication and full credit and data usage information is available by clicking on the sequence name:
  

• T. cruzi cruzi JR cl. 4 (TcI lineage)

• L. braziliensis clone M2903 (MHOM/BR/75M2903)

• C. fasciculata updated assembly

• Genomic sequence data is available under the heading "Genomic Sequences" on the home page and may be searched by species, genomic sequence IDs and BLAST.
  

• Additionally, genomic sequence data may be downloaded from the TriTrypDB download directory.

• You can now search for DNA segments defined by their chromosomal location or their nucleotide sequence (DNA motif pattern).  This new search is available under "Identify Other Data Types"; click on "Genomic Segments (DNA motif)" then select either DNA motif pattern or Genomic Location.

• We introduced a new combine operation that allows users to combine steps based on relative locations on the genome.  This enables you, for example, to return all genes that contain a specific DNA motif within 1000 nucleotides upstream of the annotated start site. Or you could return all genes that have a SNP between two strains within 500 nucleotides of the start of the gene (or return all SNPs that are located in this region relative to genes).  

• Here is an example search strategy that identifies protein coding genes with a putative RNA binding protein-like site in their 3' region. 

• Tutorials highlighting the DNA motif search and the locational relationship functionality are available.

• How and why should you register for an account
  
• How to run a text search
• How to use Favorites
• How to find a DNA motif
• How to use genomic co-location

• Whole genome shotgun sequence of Nematocida parisii strain ERTm3 generated by The Broad Institute Genome Sequencing Platform with Federal funds from the National Institute of Allergy and Infectious Diseases National under Contract No.: HHSN2722009000018C and obtained from GenBank.

• Genomic sequence data from unannotated genomes can be searched from the "Genomic Sequences" section under the heading "Identify other data types" on the home page. 
  

• You can now search for DNA segments defined by their chromosomal location or their nucleotide sequence (DNA motif pattern).  This new search is available under "Identify Other Data Types"; click on "Genomic Segments (DNA motif)" then select either DNA motif pattern or Genomic Location.

• We introduced a new combine operation that allows users to combine steps based on relative locations on the genome.  This enables you, for example, to return all genes that contain a specific DNA motif within 1000 nucleotides upstream of the annotated start site. Or you could return all genes that have a SNP between two strains within 500 nucleotides of the start of the gene (or return all SNPs that are located in this region relative to genes).  

• Here is an example search strategy that identifies protein coding genes with an AP-2 like motif within 1000 bp of their 5' end.

• Tutorials highlighting the DNA motif search and the locational relationship functionality are available.

• How and why should you register for an account
  
• How to run a text search
• How to use Favorites
• How to find a DNA motif
• How to use genomic co-location
  

• You can now search for DNA segments defined by their chromosomal location or their nucleotide sequence (DNA motif pattern).  This new search is available under "Identify Other Data Types"; click on "Genomic Segments (DNA motif)" then select either DNA motif pattern or Genomic Location.

• We introduced a new combine operation that allows users to combine steps based on relative locations on the genome.  This enables you, for example, to return all genes that contain a specific DNA motif within 1000 nucleotides upstream of the annotated start site. Or you could return all genes that have a SNP between two strains within 500 nucleotides of the start of the gene (or return all SNPs that are located in this region relative to genes).  

• Here is an example search strategy that identifies protein coding genes with an AP-2 like motif within 1000 bp of their 5' end.

• Tutorials highlighting the DNA motif search and the locational relationship functionality are available.

• How and why should you register for an account
  
• How to run a text search
• How to use Favorites
• How to find a DNA motif
• How to use genomic co-location

• P. falciparum mRNA half-life data intraerythrocytic developmental cycle (Shock et. al.) is now available as mRNA expression and half-life graphs on gene pages.  To view this data visit any gene page and scroll down to the section called "mRNA half-lives during intraerythrocytic development - 3D7 post treatment with actD" in the Expression section of any gene page.

• P. falciparum genetic diversity estimate graph is provided in the genome browser based on Nygaard et. al.

• Updated linkouts to the Malaria Parasite Metabolic Pathways (MPMP) database.  Numerous pathways have been added and updated by Dr. Hagai Ginsburg.   A full description of new pathways is available here and genes included in the MPMP database can be searched based on metabolic pathway in PlasmoDB here.

• You can now search for DNA segments defined by their chromosomal location or their nucleotide sequence (DNA motif pattern).  This new search is available under "Identify Other Data Types"; click on "Genomic Segments (DNA motif)" then select either DNA motif pattern or Genomic Location.

• We introduced a new combine operation that allows users to combine steps based on relative locations on the genome.  This enables you, for example, to return all genes that contain a specific DNA motif within 1000 nucleotides upstream of the annotated start site. Or you could return all genes that have a SNP between two strains within 500 nucleotides of the start of the gene (or return all SNPs that are located in this region relative to genes).  

• Here is an example search strategy that identifies protein coding genes with an AP-2 like motif within 1000 bp of their 5' end.

• Tutorials highlighting the DNA motif search and the locational relationship functionality are available.

• How and why should you register for an account
  
• How to run a text search
• How to use Favorites
• How to find a DNA motif
• How to use genomic co-location

• T. gondii microarray data from oocyst, bradyzoite and tachyzoite developmental stages provided by the Boothroyd and Conrad groups pre-publication.  This data was generated as part of the driving biological project bioinformatic resource funding mechanism. 
  

• To search this data, go to the "Identify Genes by Microarray Evidence section"and click on either the fold change or percentile searches under the heading "Oocyst/Tachyzoite/Bradyzoite Development (Boothroyd/Conrad)".  Here is a search that finds genes that are differentially regulated between day 0 oocysts and any of the other developmental stages from this study.  

• The first unannotated sequences from the Toxoplasma sequencing white paper are now available via ToxoDB.  You can access the genome sequence of T. gondii strains MAS, P89 and VAND from the "Genomic Sequences" section under the heading "Identify other data types" on the home page.  Genome sequences from this effort will be incorporated into ToxoDB release as they become available.  The latest updated information on the status of sequencing is available here.  The sequencing white paper is available here.

• You can now search for DNA segments defined by their chromosomal location or their nucleotide sequence (DNA motif pattern).  This new search is available under "Identify Other Data Types"; click on "Genomic Segments (DNA motif)" then select either DNA motif pattern or Genomic Location.

• We introduced a new combine operation that allows users to combine steps based on relative locations on the genome.  This enables you, for example, to return all genes that contain a specific DNA motif within 1000 nucleotides upstream of the annotated start site. Or you could return all genes that have a SNP between two strains within 500 nucleotides of the start of the gene (or return all SNPs that are located in this region relative to genes).  

• Here is an example search strategy that identifies protein coding genes with an AP-2 like motif within 1000 bp of their 5' end.

• Tutorials highlighting the DNA motif search and the locational relationship functionality are available.

• How and why should you register for an account.
  
• How to run a text search.
• How to use Favorites.
• How to find a DNA motif
• How to use genomic co-location
  

• You can now search for DNA segments defined by their chromosomal location or their nucleotide sequence (DNA motif pattern).  This new search is available under "Identify Other Data Types"; click on "Genomic Segments (DNA motif)" then select either DNA motif pattern or Genomic Location.

• We introduced a new combine operation that allows users to combine steps based on relative locations on the genome.  This enables you, for example, to return all genes that contain a specific DNA motif within 1000 nucleotides upstream of the annotated start site. Or you could return all genes that have a SNP between two strains within 500 nucleotides of the start of the gene (or return all SNPs that are located in this region relative to genes).  

• Here is an example search strategy that identifies protein coding genes with an AP-2 like motif within 1000 bp of their 5' end.

• Tutorials highlighting the DNA motif search and the locational relationship functionality are available.

• How and why should you register for an account
  
• How to run a text search
• How to use Favorites
• How to find a DNA motif
• How to use genomic co-location

• New microarray expression data for Culex quinquefasciatus and Aedes aegypti
• Updated mass spec. peptides for Anopheles gambiae available via DAS and simple browsing interface
• Anopheles funestus RNA-seq contigs available for BLAST and browsing and search
• GTF file format for use in tophat/cufflinks analysis of RNA-seq data available for download from all species.

• Histone 3 monomethyl-Lysine 4 (H3K4me1) chromatin Immunoprecipitation chip data identifying active transcriptional units.  This data was generated by Mathieu Gissot, J. Eduardo Fajardo, Louis M. Weiss, Andras Fiser and Kami Kim (Albert Einstein College of Medicine) and was graciously provided pre-publication to the Toxoplasma research community via ToxoDB.
• This data is available as genome browser tracks. An example region of the Toxoplasma genome with these tracks turned on can be accessed here.

• T. gondii (VEG) and N. caninum (Liverpool) tachyzoite RNA-sequence data.  This data was generated by Adam Reid, Mandy Sanders, Mike Quail, Matthew Berriman, Arnab Pain (Wellcome Trust Sanger Institute) Rebecca Norton, Dong Xia, Sarah Vermont and Jonathan Wastling (University of Liverpool).  This data was graciously provided pre-publication to the Toxoplasma research community via ToxoDB.

• Genes in ToxoDB may be identified using this data based on their expression percentile.  This search is available under the "Transcript Expression" section in ToxoDB.  In addition, expression coverage and percentile graphs are available on gene pages. 
  

• RNA-sequence coverage graphs may also be visualized in the genome browser.  Data has been mapped to both the VEG and ME49 genomes. 
  

• Genome sequence of Octosporea bayeri OER-3-3 described by Corradi et. al. and downloaded from Genbank (O.bayeri Genbank Record).

• Whole genome shotgun sequence of Nematocida parisii strain ERTm1 generated by The Broad Institute Genome Sequencing Platform with Federal funds from the National Institute of Allergy and Infectious Diseases National under Contract No.: HHSN2722009000018C and obtained from GenBank.
  

• This release of TriTrypDB includes a complete rebuild of the genome sequences and annotation.  Annotation improvements come from manual curation (spearheaded by GeneDB) and direct contribution of the broader kinetoplastid research community through publications and User comments on TriTrypDB gene pages.  While the annotation is current as of November 2010, newer changes at GeneDB are prominently highlighted on gene pages with linkouts to GeneDB.

• Trypanosoma brucei Lister strain 427 genome sequence and annotation provided prepublication by Dr. George Cross.  The assemblies were evaluated and annotations were transferred from the genome reference strain TREU 927 by Matthew Rogers at GeneDB.  Additional annotation performed by the AutoMagi software by Dr. Peter Myler's group at Seattle BioMed are available as a genome browser track.

• Genes may be queried based on gene IDs, text terms, EC numbers, GO terms, sequence features (length, introns, signal sequences, Pfam domains), etc.
• Genes and sequences may also be interrogated based on BLAST similarity, user-defined motifs, etc.
• Please note that Lister 427 genes assembled de-novo, rather than using TREU 927 chromosome templates, and including all VSG genes, will be available for BLAST searching and BOWTIE mapping at the Cross Lab and for BLAST searching at TriTrypDB.

• Phosphorylated cytosolic fraction peptides from bloodstream T. brucei (Nett et. al.).  Genes with evidence of protein expression based on this experiment can be searched via the Mass Spec. As usual, results from this experiment can be combined with results from other searches -- for example, find all genes with evidence of phosphorylated peptides that are also likely kinases -- visit this link (or share it with others) to see the results of this search.

• TriTrypDB now provides linkouts to LeishCyc (database of Leishmania metabolic pathways) from relevant Leishmania gene pages.  The linkouts are available in the external links section of gene pages --  for example: LmjF.07.1070

• A draft assembly of the genome sequence of Trypanosoma cruzi Esmeraldo strain cl3.  The sequence data has been graciously made available prepublication to the community via TriTrypDB by Dr. Gregory A. Buck (Virginia Commonwealth University) and The Genome Center at Washington University School of Medicine.  Total sequence coverage was ~63X (fragments ~47X, 3 Kb paired end (PE) ~11X, 8 Kb PE ~5X) using a genome size estimate of 40 Mbp. The combined sequence reads were assembled using the Newbler software (Roche 454). The first draft assembly was referred to as T_cruzi_Esmeraldo_5.1 and has been cleaned of contaminants. The assembly is made up of a total of 23,808 scaffolds with an N50 scaffold length of over 52kb (N50 contig length for the 31,945 contigs was 3.3kb). The assembly spans 35.5Mb. This assembly is subject to change due to ongoing assembly improvement efforts. Complete data source information is available here.

• Genomic sequence data is available under the heading "Genomic Sequences" on the home page and may be searched by species, genomic sequence IDs and BLAST.
  

• Additionally, genomic sequence data may be downloaded from the TriTrypDB download directory.

• L. braziliensis secretome proteomics data from Cuervo et. al.  This data can be searched from the Mass spec. evidence search page under the heading "Protein Expression" -- listed under Leishmania braziliensis.  In addition, peptide evidence is displayed on gene pages in the Protein Section and in the genome browser by turning on the track specific for this data.

• L. major exosome proteomics data from Silverman et. al.  This data can be searched from the Mass spec. evidence search page under the heading "Protein Expression" -- listed under Leishmania major  In addition, peptide evidence is displayed on gene pages in the Protein Section and in the genome browser by turning on the track specific for this data.

• L. infantum differentiation microarray data from Rochette et. al.  This data can be searched from the Microarray Evidence search page under the heading "Axenic vs Intracellular Amastigotes Comparison (Papadopoulou)".  This data can be searched based on fold change differences between life stages examined or based on percentile expression.   As usual, searches may be combined with other searches in TriTrypDB -- for example this search combines a search of this data (gene upregulated in amastigotes v. promastigotes) with a GO Term search.  In addition, microarray data is displayed on individual gene pages as graphs and a table in the expression section.  You can click on "show" to see the table and you can select the type of graph to see (fold change graph, percentile graph or both).

• A draft assembly of the genome sequence of Leishmania major (strain SD 75.1).  The sequence data has been graciously made available prepublication to the community via TriTrypDB by Dr. Stephen Beverley.  The assembly spans 30.8 Mb and is made up of a total of 1904 scaffolds with an N50 scaffold length of over 691kb (N50 contig length for the 4009 contigs is 27kb). Complete data source information is available here.

• Genomic sequence data is available under the heading "Genomic Sequences" on the home page and may be searched by species, genomic sequence IDs and BLAST.
  

• Additionally, genomic sequence data may be downloaded from the TriTrypDB download directory.

• Gene names from GeneDB are now included as part of the product description field on gene pages in TriTrypDB.  

• E. histolytica DS4
• E. histolytica KU50
• E. histolytica MS96
• E. histolytica HM-1:CA
• E. histolytica KU48
• E. histolytica KU27
  
  

• Genomic sequence data is available under the heading "Genomic Sequences" on the home page and may be searched by species, genomic sequence IDs and BLAST.
  
• Additionally, genomic sequence data may be downloaded from the AmoebaDB download directory.
  
  

• 2010 MPM poster presented by Linda I. Hannick.
• 2010 presentation at the Montreal Amebiasis meeting by Lis Caler.

• P. falciparum blood stage proteomics data (trophozoites and early and mature gametocytes) from Silvestrini et. al.  This data can be searched from the Mass spec. evidence search page under the heading "Protein Expression" -- listed under Plasmodium falciparum and selecting "Blood Stage Proteome - Trophozoites, Early Gametocytes (gct I/II) and/or Mature Gametocytes (gct V)".  In addition, peptide evidence is displayed on gene pages in the Protein Section and in the genome browser by turning on the track specific for this data.  An example search strategy that identifies genes that have mass spec evidence in the early gametocytes but not in trophozoites or mature gametocytes can be accessed and modified here.
  

• You can now add publications to your user comments using their Digital Object Identifier (DOI) numbers.  To view a list of all genes that have a user comment in PlasmoDB, click here.

• You can view microarray oligo mapping for all arrays with data in PlasmoDB.  Oligo mapping can be viewed in the Genome Browser by turning on tracks under the heading "Expression Microarray Probes".
  

• Giardia intestinalis microarray data during encystation from Adrian Hehl's group (Morf et. al.).  Three types of searches can be performed to interrogateinterrogatedinterrogatedinterrogatedinterrogatedinterrogated this data and are available in the microarray search page.  As an example, one may ask for all genes that are differentially regulated 7 hours post encystation (under both encystation methods used in this study).  To see the results of this question please follow the shared strategy here.  Gene pages also contain a graphical representation of the microarray results.  

• Improved organization of the microarray search page.
• The search strategy window is now resizable.

• Proteomics data from E. histolytica phagosomes of various degrees of maturation (Boettner et. al.).  This data can be searched in AmoebaDB from the Mass Spec. search page and results can be integrated with other search types.  An example search strategy that integrates different search types can be viewed here.  This strategy asks for all E. histolytica genes  with phagosome proteomic evidence, that contain transmembrane domains and  contain a "kinase" PFAM domain. 
  
• Gene that have evidence of protein expression also have a graphical representation of the peptide hits on their respective gene pages (mousing over the graphics provides additional information such as peptide sequence).  Here is a link to a gene page with proteomics evidence -- scroll down to the "Protein" section and show "Protein features".  Note that samples are color coded.
  
• Proteomics data can also be visualized in the genome browser.  This link shows a 200Kb genomic region with the gene models and proteomics track turned on. 
  

• The search strategy window is now resizable.

• Genome sequence of Crithidia fasciculata (strain/isolate Cf-C1).  The sequence data has been graciously made available prepublication to the community via TriTrypDB by Dr. Stephen Beverley.  The C. fasciculata strain was obtained from Dr. Larry Simpson, University of California, Los Angeles.  Genomic DNA was generated by Drs. Natalia Akopyants, Lon-Fye Lye and Stephen Beverley, Washington University School of Medicine.  A combination of next-generation sequencing and Sanger reads were produced for a draft assembly by The Genome Center at Washington University.  Complete data source information is available here.
• Genomic sequence data is available under the heading "Genomic Sequences" on the home page and may be searched by species, genomic sequence IDs and BLAST.
  
• Aditionally, genomic sequence data may be downloaded from the TriTrypDB download directory.
  

• Additional ChIP-sequence data is available via the genome browser provided by Drs. George Cross, Nicolai Siegel and Jessica Wright (Wright et. al. and Siegel et. al.).  An example genome browser view with ChIP-seq track turned on may be viewed here.

• Improved organization of the microarray search page.
• The search strategy window is now resizable.

• Anncaliia algerae
  
• Edhazardia aedis
• Nosema bombycis
• Vittaforma corneae

• The search strategy window is now resizable.

• Genes can be identified based on the fold change in their expression between selected time points from the experiment using the T.g. Cell Cycle (fold change).
• Genes can be identified based on their maximal or minimal expression among selected time points using the T.g. Cell Cycle (exprn timing) search.
• Genes with a similar expression profile throughout the cell cycle compared to an input gene can be identified using the T.g. Cell Cycle (similarity) search.  For example, genes that have a similar expression profile throughout the cell cycle compared to a putative nucleoporin can be identified as illustrated by this search strategy.  A graphical representation of the search results is presented along with the list of results showing the expression profile of the reference gene and each of the comparator genes.

• Improved organization of the microarray search page.
• The search strategy window is now resizable.

• Updated sequence and annotation for Plasmodium falciparum, P. chabaudi, P. knowlesi and P. berghei was obtained from the Pathogen Sequencing Unit at the Wellcome Trust Sanger Institute.  Additional details may be viewed here.

• Updated linkouts to the Malaria Parasite Metabolic Pathways (MPMP) database.  Numerous pathways have been added and updated by Dr. Hagai Ginsburg.   A full description of new pathways is available here and genes included in the MPMP database can be searched based on metabolic pathway in PlasmoDB here.
  

• Plasmodium falciparum, P. vivax, P. yoelii, P. berghei and P. chabaudi predicted ApiAP2 transcription-factor (TF) binding site data.  This data was graciously provided prepublication by Dr. Manuel Llinas.  Gene with predicted binding sites to each ApiAP2 TF may be identified using the TF binding site search available via the Transcript Expression section of PlasmoDB.  Search parameter such as distance from the 5' end, number of TF binding sites and probability score can be adjusted as needed.  In addition, TF binding sites can be viewed in the genome browser with additional information available when mousing over TF binding site graphics.  An example genome browser page may be viewed here.

• P. falciparum RNA-sequence data from the intraerythrocytic life cycle.  This data was graciously provided prepublication to the community via PlasmoDB by Dr. Rich�rd B�rtfai, Wieteke A.M. Hoeijmakers and Dr. Hendrik G. Stunnenberg.  Searches against this data may be accessed from the RNA-seq evidence section in the Transcript Expression section of PlasmoDB.  RNA-seq data may also be viewed on individual gene pages where a graphical representation of the gene's expression profile throughout the time points of this study is presented.   In addition,  RNA-seq coverage graphs can be viewed through the PlasmoDB genome browser.
  

• P. falciparum ChIP-sequence data from the intraerythrocytic life cycle.  ChIP was performed using antibodies to H2A.Z, H3K9ac & H3K4me3. This data was graciously provided prepublication to the community via PlasmoDB by Dr. Rich�rd B�rtfai, Wieteke A.M. Hoeijmakers and Dr. Hendrik G. Stunnenberg.  This data can be viewed through the PlasmoDB genome browser.

• P. falciparum RNA-sequence data of lab-adapted field parasites from malaria-infected pregnant women and children.  This data was graciously provided prepublication to the community via PlasmoDB by Drs. Marissa Vignali and Patrick E. Duffy.  Searches against this data may be accessed from the RNA-seq evidence section in the Transcript Expression section of PlasmoDB.  RNA-seq data may also be viewed on individual gene pages where a graphical representation of the gene's expression profile throughout the time points of this study is presented.   In addition,  RNA-seq coverage graphs can be viewed through the PlasmoDB genome browser.

• Improved organization of the microarray search page.
• The search strategy window is now resizable.

• The Basket and Favorites functionality has been extended to include all record classes.
• Queries have been optimized to increase site performance.
• A number of bugs have been fixed.

• Giardia intestinalis microarray data during host parasite interaction.  This data was graciously provided prepublication by Emma Ringqvist and Staffan Sv�rd (Uppsala University, Sweden).
• Manually curated SAGE tag data provided by Andrew McArthur and described by Birkeland et. al.
  

• Digital gene expression data for T. brucei procyclic and blood form stages provided by Annette Macleod.
  Digital gene expression analysis of two life cycle stages of the human-infective parasite, Trypanosoma brucei gambiense reveals differentially expressed clusters of co-regulated genes. Veitch NJ, Johnson PC, Trivedi U, Terry S, Wildridge D, MacLeod A. BMC Genomics. 2010 Feb 22;11:124.
• Links have been added to the TcSNP database of genetic variation in T. cruzi from T. cruzi gene record pages.

• Sequence and annotation of E. bieneusi are described in the publication "Genomic survey of the non-cultivatable opportunistic human pathogen, Enterocytozoon bieneusi" and were obtained from GenBank.
  
• Genome sequence of E. bieneusi can be compared to the sequences of  E. cuniculi and E. intestinalis using synteny.
• E. bieneusi genes may be identified based on text terms, ID #, GO terms, chromosomal location, BLAST, sequence features (length/MW, exons, signal sequences, Pfam domains, user-defined motifs), orthology, etc.

• Gene expression in Entamoeba histolytica cysts and trophozoites.  This study is described by Ehrenkaufer et. al.
  
• Impact of intestinal colonization and invasion on the Entamoeba histolytica transcriptome This study is described by Gilchrist et. al.
  

• A proteomics dataset for P. falciparum from 42 and 48 hrs post infection kindly provided prepublication by Paul Bowyer and Matthew Bogyo, Stanford University School of Medicine.
• P. falciparum SNP calls for 186 culture adapted strains provided by Jianbing Mu and Xinzhuan Su, NIH.
  Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs. Nat. Genet. 2010 Mar;42(3):268-71 Mu et al.

• The Basket and Favorites functionality has been extended to include all record classes.
• Queries have been optimized to increase site performance.
• A number of bugs have been fixed.

• The Basket and Favorites functionality has been extended to include all record classes.
• Queries have been optimized to increase site performance.
• A number of bugs have been fixed.

1. "My Basket" allows one to cherry pick genes and add them to the basket for subsequent conversion into a step in a strategy.  The basket is accessible from the gray menu bar and the number of items in your basket is indicated.


2. Weighted searches allows you to assign an arbitrary weight to the searches (steps) in your search strategy making it possible for you to view a ranked list of your results.  
Here is an example of the same strategy looking for putative secreted proteinases upregulated in T. cruzi epimastigotes.  Notice that you have a larger number of results with weighting and those can be sorted based on the sum of the weights, giving a ranked list of results.

Putative vaccine candidates (unweighted)

Putative vaccine candidates (Weighted)


3. "My Favorites" (new in this release) allows you to bookmark and organize genes you access frequently.  A tutorial on how to use this feature is available here. 

1. "My Basket" allows one to cherry pick genes and add them to the basket for subsequent conversion into a step in a strategy.  The basket is accessible from the gray menu bar and the number of items in your basket is indicated.


2. Weighted searches allows you to assign an arbitrary weight to the searches (steps) in your search strategy making it possible for you to view a ranked list of your results.  
Here is an example of the same strategy looking for putative secreted enzymes.  Notice that you have a larger number of results with weighting and those can be sorted based on the sum of the weights, giving a ranked list of results.

Putative secreted enzymes (unweighted)

Putative secreted enzymes (Weighted)


3. "My Favorites" allows you to bookmark and organize genes you access frequently.  A tutorial on how to use this feature is available here. 

1. "My Basket" allows one to cherry pick genes and add them to the basket for subsequent conversion into a step in a strategy.  The basket is accessible from the gray menu bar and the number of items in your basket is indicated.


2. Weighted searches allows you to assign an arbitrary weight to the searches (steps) in your search strategy making it possible for you to view a ranked list of your results.  

1. "My Favorites" allows you to bookmark and organize genes you access frequently.  A tutorial on how to use this feature is available here. 

• PiggyBac insertion sites in P. falciparum (NF54) from Balu et. al. are available via the genome browser.  To view insertion sites turn on the track called "P. falciparum piggyBac Transposable Elements" under the heading "Insertions".  Here is a quick link to the genome browser with a region with insertions: piggyBac insertions in chromosome 11. 


• ChIP-chip data using histone H4 antibodies from Westenberger et. al. are available via the genome browser under the ChIP on chip heading. You may view tracks for different RBC life stages as in this example.


• Nucleosome positioning data from Ponts et. al.  are available via the genome browser under the ChIP-seq heading.  You may view tracks for different time points during the RBC life cycle as in this example.

1. "My Basket" allows one to cherry pick genes and add them to the basket for subsequent conversion into a step in a strategy.  The basket is accessible from the gray menu bar and the number of items in your basket is indicated.


2. Weighted searches allows you to assign an arbitrary weight to the searches (steps) in your search strategy making it possible for you to view a ranked list of your results.  
Here is an example of the same strategy looking for putative vaccine candidates.  Notice that you have a larger number of results with weighting and those can be sorted based on the sum of the weights, giving a ranked list of results.

Putative vaccine candidates (unweighted)

Putative vaccine candidates (Weighted)


3. "My Favorites" (new in this release) allows you to bookmark and organize genes you access frequently.  A tutorial on how to use this feature is available here. 


4. We now provide prominent linkouts to GeneDB from PlasmoDB gene pages when there is an update in GeneDB not yet available in PlasmoDB.  This feature enables PlasmoDB users to have easy access to the most up-to-date information.  It is important to highlight that your comments on gene pages in PlasmoDB constitute one of the tools made available to the annotators at GeneDB to improve and enhance the genome annotation.

1. "My Basket" allows one to cherry pick genes and add them to the basket for subsequent conversion into a step in a strategy.  The basket is accessible from the gray menu bar and the number of items in your basket is indicated.


2. Weighted searches allows you to assign an arbitrary weight to the searches (steps) in your search strategy making it possible for you to view a ranked list of your results.  
Here is an example of the same strategy looking for secreted bradyzoite genes under diversifying selection.  Notice that you have a larger number of results with weighting and those can be sorted based on the sum of the weights, giving a ranked list of results.

Putative secreted brady (unweighted)

Putative secreted brady (Weighted)


3. "My Favorites" allows you to bookmark and organize genes you access frequently.  A tutorial on how to use this feature is available here. 

1. "My Basket" allows one to cherry pick genes and add them to the basket for subsequent conversion into a step in a strategy.  The basket is accessible from the gray menu bar and the number of items in your basket is indicated.


2. Weighted searches allows you to assign an arbitrary weight to the searches (steps) in your search strategy making it possible for you to view a ranked list of your results.  
Here is an example of the same strategy looking for putative secreted enzymes.  Notice that you have a larger number of results with weighting and those can be sorted based on the sum of the weights, giving a ranked list of results.

Putative secreted enzymes (unweighted)

Putative secreted enzymes (Weighted)


3. "My Favorites" allows you to bookmark and organize genes you access frequently.  A tutorial on how to use this feature is available here. 

1. "My Basket" allows one to cherry pick genes and add them to the basket for subsequent conversion into a step in a strategy.  The basket is accessible from the gray menu bar and the number of items in your basket is indicated.


2. Weighted searches allows you to assign an arbitrary weight to the searches (steps) in your search strategy making it possible for you to view a ranked list of your results.  
Here is an example of the same strategy looking for putative secretory enzymes.  Notice that you have a larger number of results with weighting and those can be sorted based on the sum of the weights, giving a ranked list of results.

Putative secretory enzyme (unweighted)

Putative secretory enzyme (Weighted)


3. "My Favorites" (new in this release) allows you to bookmark and organize genes you access frequently.  A tutorial on how to use this feature is available here. 

1. "My Basket" allows one to cherry pick genes and add them to the basket for subsequent conversion into a step in a strategy.  The basket is accessible from the gray menu bar and the number of items in your basket is indicated.


2. Weighted searches allows you to assign an arbitrary weight to the searches (steps) in your search strategy making it possible for you to view a ranked list of your results.  
Here is an example of the same strategy looking for putative secreted enzymes.  Notice that you have a larger number of results with weighting and those can be sorted based on the sum of the weights, giving a ranked list of results.

Putative secreted enzymes (unweighted)

Putative secreted enzymes (Weighted)


3. "My Favorites" allows you to bookmark and organize genes you access frequently.  A tutorial on how to use this feature is available here. 


4. A community annotation field has been added to the text search page.  This makes it possible for the Giardia research community to provide expert bulk annotations that would ultimately results in changes in the GenBank record and official annotation.  Currently, there are 164 community annotations provided by Rod Adam concerning VSPs.  To view community annotations go to the text search page in GiardiaDB and limit your search to the "Community annotation".  To view all genes that have a community annotation associated with them simply enter the wild card "*" in the text search field.  The annotation itself is prominently displayed on the gene pages right under the product name.  You can also click on the comment ID to retrieve additional information.
5. A file including assignment of contigs to chromosomes has been made available by Hilary Morrison pre-publication in the community file section of GiardiaDB.  Links to the file are available on all contig pages.

• Sequence and annotation for Encephalitozoon cuniculi and E. intestinalis (graciously provided prepublication by Patrick Keeling's group)
• Genome sequence alignments, permitting comparative genomic analysis of synteny between E. cuniculi and E. intestinalis.
• Expressed sequence tag data for E. cuniculi.
• 'User Comments' may be added to any gene page, enhancing available annotation. Such comments become immediately visible and searchable by others.
• Identification of genes based on text terms, ID #, GO terms, chromosomal location, BLAST, sequence features (length/MW, exons, signal sequences, Pfam domains, user-defined motifs), orthology, etc.
  

• Sequence and annotation for Entamoeba histolytica, E. dispar and E. invadens.
• Genome sequence alignments, permitting comparative genomic analysis of synteny between Entamoeba species.
• Expressed sequence tag data for E. histolytica and E. dispar.
• 'User Comments' may be added to any gene page, enhancing available annotation. Such comments become immediately visible and searchable by others.
• Identification of genes based on text terms, ID #, GO terms, EC #, chromosomal location, BLAST, sequence features (length/MW, exons, signal sequences, Pfam domains, user-defined motifs), orthology, etc.
• Support for integrated searches, via the 'search strategy builder'.  Strategies can be stored and shared with others by logging into AmoebaDB. For an example, open this sample strategy that combines multiple searches, in your browser.

• The gray tool bar at the top of all CryptoDB web pages has been enhanced to include a link to the "My Basket" feature including an indication of how may items are in the basket.
• The genome browser has been updated to version 1.7, which offers enhanced features and stability. Now you can select a span and send the sequence to ncbi for blasting!
• Weighted searches are now available.  This feature allows you to assign an arbitrary weight to the searches (steps) in your search strategy making it possible for you to view a ranked list of your results. 

• Microarray data from of Minning et. al. of T. cruzi life cycle stages (trypomastigotes, amastigotes, epimastigotes, and metacyclic trypomastigotes). For additional details please see the publication http://www.ncbi.nlm.nih.gov/pubmed/19664227
• Microarray data from Queiroz et. al. of T. brucei expression profile during in vitro differentiation from slender bloodstream forms to stumpy procyclic forms. For additional details please see the publication  http://www.ncbi.nlm.nih.gov/pubmed/19857263 
• Microarray data from Kabani et. al. of rodent-derived T. brucei  pleomorphic slender forms, stumpy forms and at 1h, 6h, 18h, and 48h through synchronous in vitro differentiation to procyclic forms.  For additional details please see the publication  http://www.ncbi.nlm.nih.gov/pubmed/19747379
• Microarray data from Jensen et. al. of five different T. brucei life cycle stages. For additional details please see the publication  http://www.ncbi.nlm.nih.gov/pubmed/19840382
• Microarray data from Estevez of T. brucei depleted of the RNA-binding protein TbDRBD3.  For additional details please see the publication  http://www.ncbi.nlm.nih.gov/pubmed/18611951

• Access all microarray searches in TriTrypDB
• Expression profile graphs are also available on gene pages.

• RNA sequence data provided pre-publication by George Cross of blood and procyclic forms of T. brucei.  Expression profiles based on RNA-seq data can be viewed in the genome browser, on gene pages or searched in the Genes by RNA-Seq page.

• The gray tool bar at the top of all TriTrypDB web pages has been enhanced to include a link to the "My Basket" feature including an indication of how may items are in the basket.
• The genome browser has been updated to version 1.7, which offers enhanced features and stability. 
• Weighted searches are now available.  This feature allows you to assign an arbitrary weight to the searches (steps) in your search strategy making it possible for you to view a ranked list of your results. 

• The gray tool bar at the top of all GiardiaDB web pages has been enhanced to include a link to the "My Basket" feature including an indication of how may items are in the basket.
• The genome browser has been updated to version 1.7, which offers enhanced features and stability. 
• Weighted searches are now available.  This feature allows you to assign an arbitrary weight to the searches (steps) in your search strategy making it possible for you to view a ranked list of your results. 

• T. brucei chromatin immunoprecipitation sequencing data presented as Genome Browser tracks.  Data from four histone variants (H2AZ, H2BV, H3V, and H4V) can be viewed.  To see an example of this, please click here. To read more about this data please examine the following publication: Siegel TN, Hekstra DR, Kemp LE, Figueiredo LM, Lowell JE, Fenyo D, Wang X, Dewell S, Cross GA. Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei. Genes Dev. 2009 May 1;23(9):1063-76.
• Updated Sequence and assembly for T. brucei 927 and updated annotation for all other organisms in TriTrypDB.
• The following new genome sequence and annotation have been incorporated into TriTrypDB and can be searched and compared to each other:
• Trypanosoma brucei gambiense
• Trypanosoma congolense  
• Trypanosoma vivax  
• Leishmania mexicana (available as sequence and assembly only, annotation will be incorporated in the February release of TriTrypDB)

• This release features the addition of a "My Basket" tool.  This feature allows you to select various genes from your searches and add them to your basket (much like a shopping cart).  To add genes to your basket simply click on the basket icon in a result list or on a gene page.  A green basket icon indicates that a genes is already in your basket.  You can easily convert your basket to a strategy to save it and perform additional searches or combine it with one of your already existing strategies.  Please note that using the basket feature requires you to login first.
• The multiple sequence alignment tool available from gene pages has been updated to allow the selection of the organisms to be aligned.  The multiple sequence aligner is available on gene pages right under the genomic context view.
• Web services have been implemented to receive weekly updates from GeneDB to provide a more rapid account for updated genes.

• P. falciparum transcriptome sequencing (RNA-seq) profiles.  This data was graciously provided to PlasmoDB prepublication and will soon appear in press: New insights into the blood stage transcriptome of Plasmodium falciparum using RNA-Seq.  Thomas D. Otto, Daniel Wilinski, Sammy Assefa, Thomas M. Keane, Louis R. Sarry, Ulrike Bohme, Jacob Lemieux, Bart Barrell, Arnab Pain, Matthew Berriman, Chris Newbold, Manuel Llinas.  Molecular Microbiology (in press).  You can search for genes based on this data by going to the "P. falciparum transcriptome sequencing (RNA-seq) profiles" search under "Transcript Expression" in PlasmoDB.

• P. falciparum transcription profile of wild-type and Sir2a and Sir2b knock-out parasites.  Using this search you can find genes that are differentially expressed between wild-type and knock-out parasites during the intraerythrocytic life-cycle.  You can search for genes based on this data by going to the "Microarray Evidence" search under "Transcript Expression" in PlasmoDB.   Details of this study can be found here:  Tonkin CJ, Carret CK, Duraisingh MT, Voss TS, Ralph SA, Hommel M, Duffy MF, Silva LM, Scherf A, Ivens A, Speed TP, Beeson JG, Cowman AF. Sir2 paralogues cooperate to regulate virulence genes and antigenic variation in Plasmodium falciparum. PLoS Biol. 2009 Apr 14;7(4):e84.

• Transcription profiling of Plasmodium falciparum after exposing drug-selected mutants to short term CQ treatment.  Identify genes differentially expressed during chloroquine treatment.  You can search for genes based on this data by going to the "Microarray Evidence" search under "Transcript Expression" in PlasmoDB. Details of this study can be found here: Jiang H, Patel JJ, Yi M, Mu J, Ding J, Stephens R, Cooper RA, Ferdig MT, Su XZ. Genome-wide compensatory changes accompany drug- selected mutations in the Plasmodium falciparum crt gene. PLoS One 2008 Jun 25;3(6):e2484.

• P. falicparum HP1 chromatin immunoprecipitation data.  You can search for genes based on this data by going to the "P.f ChIP on chip evidence" search under "Transcript Expression" in PlasmoDB. Details of this study can be found here: Flueck C, Bartfai R, Volz J, Niederwieser I, Salcedo-Amaya AM, Alako BT, Ehlgen F, Ralph SA, Cowman AF, Bozdech Z, Stunnenberg HG, Voss TS.  Plasmodium falciparum heterochromatin protein 1 marks genomic loci linked to phenotypic variation of exported virulence factors. PLoS Pathog. 2009 Sep;5(9):e1000569. Epub 2009 Sep 4.

• Chromatin immunoprecipitation to identify histone modifications (H3K9me3, H3K9Ac, H3K4me3, H4K20me3) in P. falciparum wild type and Sir2 knock-outs. You can search for genes based on this data by going to the "P.f ChIP on chip evidence" search under "Transcript Expression" in PlasmoDB. Details of this study can be found here:  Lopez-Rubio JJ, Mancio-Silva L, Scherf A. Genome-wide analysis of heterochromatin associates clonally variant gene regulation with perinuclear repressive centers in malaria parasites. Cell Host Microbe. 2009 Feb 19;5(2):179-90.

• Genome sequence and annotation of Giardia intestinalis assemblage B isolate GS.  For further information please refer to the publication: Draft genome sequencing of giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species? PLoS Pathog. 2009 Aug;5(8):e1000560 Franz�n et al.

• Sequence and annotation of Giardia assemblage E isolate P15 was provided by J. Jerlstrom-Hultqvist. O. Franzen, E. Castro, J. Ankarklev, D. Palm, J. O. Andersson, S.G. Svard and B. Andersson (Karolinska Institutet, Stockholm, Sweden and Uppsala University, Uppsala, Sweden). The genome sequence and annotation was graciously provided to GiardiaDB prepublication.  

• Additional stress induction microarray data graciously provided by Cornelia Spycher and Adrian Hehl prepublication (University of Z�rich, Switzerland).  Genes may be identified based on their expression profile by running one of the microarray searches and results may be combined with other searches in GiardiaDB.

• 1012 genes from Giardia lamblia assemblage A isolate WB have been undeprecated based on synteny to assemblage B and E genomes.

• Representation of SAGE tag data on gene pages has been improved providing graphical representation of tag counts over the life cycle of the parasite.

• 2-day alkaline or compound 1 differentiation of T. gondii types I (GT1), II (Me49B7) and III (CTG) strains provided by Michael Behnke and Michael White.  For study details please see the following reference: The transcription of bradyzoite genes in Toxoplasma gondii is controlled by autonomous promoter elements. Mol. Microbiol. 2008 Jun;68(6):1502-18 Behnke et al.

• 2-day alkaline differentiation time course of T. gondii type II (Prugniaud) strain provided by Matt Anderson and John Boothroyd.

• 3-day alkaline, CO2 starvation or sodium nitroprusside differentiation of T. gondii types I (RH) or II (Prugniaud) strains provided by Paul Davis and David Roos.

• 14-day CO2 starvation differentiation of T. gondii type II (Prugniaud) or III (VEG) strains provided by Paul Davis, Florence Dzierszinski and David Roos.

This release of TriTrypDB includes a new ChIP-chip experiment identifying regions of active transcription in L. major from Thomas et. al. "Histone acetylations mark origins of polycistronic transcription in Leishmania major". The data are available as Genome Browser tracks. For an example click here.

We anticipate a more significant release for TriTrypDB in late December which will include updated annotations for all the TriTryp genomes as well as three additional kinetoplastid genomes from GeneDB.
14 November 2009

• P.  falciparum and P. vivax proteomics from clinical samples graciously provided prior to publication by Dr. Utpal Tatu (Department of Biochemistry, Indian Institute of Science, Bangalore, India). This data may be accessed using the "Identify Genes based on Mass Spec. Evidence" query and combined with other searches in PlasmoDB.

• Transform a search into its orthologs from other species in the EuPathDB family of databases.
• Edit any step in a strategy and see results change dynamically.
• Share strategies with your colleagues via email.
• Login to store your history of strategies and browse them at any time in the future.

• C. parvum mitochondrial fraction proteomics provided prepublication by Lorenza putignani.

• Now after you perform a BlastN against genomic sequence you can link from the blast output to the correct coordinates in the genome browser.  This allows you to explore annotation and other functional data in relation to your BLAST hits.
• The type ahead feature has been implemented for GO term, EC number and Interpro domain searches.
• You can now edit or delete your user comments.
• You can now modify your user profile, change your password or your email address.

• Identify Genes based on Orthology Phylogenetic Profile:  For example you may ask for genes in T. vaginalis that do not have orthologs in mammals.  Click here to explore this feature.
• A table of paralogs (if any) is now available on gene pages allowing you to view expanded gene families -- See TVAG_386080 for example (scroll down to the Orthologs and Paralogs Table).
• Now after you perform a BlastN against genomic sequence you can link from the blast output to the correct coordinates in the genome browser.  This allows you to explore annotation and other functional data in relation to your BLAST hits.
• The type ahead feature has been implemented for GO term, EC number and Interpro domain searches.
• You can now edit or delete your user comments.
• You can now modify your user profile, change your password or your email address.

• G. intestinalis mitosome enriched fraction proteomics provided by Jan Tachezy and described in Rada et. al.
• Giardia isolate data from GenBank are now included -- search for isolates based on many criteria such as geographic location, submitter name, isolation source and/or host.  Also, generate nucleotide sequence alignments of isolates you select, and BLAST your sequence against the isolate database.
  

• Now after you perform a BlastN against genomic sequence you can link from the blast output to the correct coordinates in the genome browser.  This allows you to explore annotation and other functional data in relation to your BLAST hits.
• A table of paralogs (if any) is now available on gene pages allowing you to view expanded gene families -- See GL50803_15158 for example (scroll down to the Orthologs and Paralogs Table).
• The type ahead feature has been implemented for GO term, EC number and Interpro domain searches.
• You can now edit or delete your user comments.
• You can now modify your user profile, change your password or your email address.

• New T. cruzi genome assembly as described in the publication by Weatherly and colleagues.
• T. cruzi reservosome proteomics data (Sant'Anna et. al.).
• T. cruzi insect form proteomics data (Cordero et. al.).
• L. infantum proteomics data set from Dr. Marc Ouellette's group (provided prepublication).
• Genome-wide analysis of mRNA abundance in two life-cycle stages of T. brucei and identification of trans-splicing and polyadenylation sites. RNA-seq (T. Nicolai Siegel, Doeke R. Hekstra, Xuning Wang, Scott Dewell and George A. M. Cross, provided prepublication) -- this data can be viewed as tracks in the genome browser, click here for an example.

• Now after you perform a BlastN against genomic sequence you can link from the blast output to the correct coordinates in the genome browser.  This allows you to explore annotation and other functional data in relation to your BLAST hits.
• The type ahead feature has been implemented for GO term, EC number and Interpro domain searches.
• You can now edit or delete your user comments.
• You can now modify your user profile, change your password or your email address.

• P.  falciparum intraerythrocytic expression profiles from infected patients (Lemieux et. al.) -- data available on gene pages, for example, click here and scroll down to the expression section.

• Now after you perform a BlastN against genomic sequence you can link from the blast output to the correct coordinates in the genome browser.  This allows you to explore annotation and other functional data in relation to your BLAST hits.
• Linkouts to Gene Ontology annotation predictions at Plasmodraft have been updated. (Br�h�lin et. al.).
• Linkouts to the Malaria Parasite Metabolic Pathways resource (Hagai Ginsburg).
• The type ahead feature has been implemented for GO term, EC number and Interpro domain searches.
• You can now edit or delete your user comments.
• You can now modify your user profile, change your password or your email address.

This release includes new and updated data sets, a new user interface with added functionality and a graphical strategy system for building complex searches.

The new user interface contains many new features including:

• A new search strategy interface that enables users to more easily construct complex searches.
• 'User Comments' have been updated to enable submission of supporting evidence including pubmed identifiers and images (or other files). Comments may be added to any gene or sequence page, enhancing available annotation.
• Files can now be uploaded and provided to the community via the file repository section.

New and updated Data:

• C. parvum KSU-1 normalized sporozoite EST sequences (provided prepublication by Jessica Kissinger).

This release features a new user interface with added functionality and a graphical strategy system for building complex searches.

The new user interface contains many new features including:

• A new search strategy interface that enables users to more easily construct complex searches.
• 'User Comments' have been updated to enable submission of supporting evidence including pubmed identifiers and images (or other files). Comments may be added to any gene or sequence page, enhancing available annotation.
• Files can now be uploaded and provided to the community via the file repository section.

The previous version of GiardiaDB may still be accessed here.
14 July 2009

This release includes several new and updated data sets (many prepublication), a new user interface with added functionality and a graphical strategy system for building complex searches.

The new user interface contains many new features including:

• A new search strategy interface that enables users to more easily construct complex searches.
• 'User Comments' have been updated to enable submission of supporting evidence including pubmed identifiers and images (or other files). Comments may be added to any gene or sequence page, enhancing available annotation.
• Files can now be uploaded and provided to the community via the file repository section.

New and updated Data:

• ChIP-chip centromere identification (Prepublication from Mathieu Gissot, Carrie F. Brooks, Boris Striepen, Kami Kim).
• Isolate data typed based on sequence (from Genbank and David Sibley) or RFLPs (from Chunlei Su).
• Whole genome sequence of the natural recombinant Toxoplasma gondii strain TgCkUg2 and SNP calls (Bontell et. al.).

The previous version of ToxoDB may still be accessed here.
14 July 2009

This release features a new user interface with added functionality and a graphical strategy system for building complex searches.

The new user interface contains many new features including:

• A new search strategy interface that enables users to more easily construct complex searches.
• 'User Comments' have been updated to enable submission of supporting evidence including pubmed identifiers and images (or other files). Comments may be added to any gene or sequence page, enhancing available annotation.
• Files can now be uploaded and provided to the community via the file repository section.

The previous version of TrichDB may still be accessed here.
14 July 2009

• The L. tarentolae genome has been provided by the CIHR Group on host pathogen interactions and is available for similarity searches and browsing for open reading frames and BLASTX alignments against the NR protein database.
• A microarray experiment examining the axenic promastigote-to-amastigote differentiation of L. donovani was provided by researchers at the Seattle Biomedical Research Institute and Technion Institute and is available for query and display on record pages.
• A new search strategy interface that enables users to more easily construct complex searches is released for the first time in TriTrypDB 1.1.
• 'User Comments' have been updated to enable submission of supporting evidence including pubmed identifiers and images (or other files). Comments may be added to any gene or sequence page, enhancing available annotation. Such comments are visible and searchable by others, and are automatically forwarded to the annotation team for incorporation into the official annotation
  
• Files can now be uploaded and provided to the community via TriTrypDB.

The previous version of TriTrypDB may still be accessed here.
14 July 2009

The EuPathDB team is happy to announce the release of PlasmoDB 6.0.

This release includes several new and updated data sets (many prepublication), a new user interface with added functionality and a graphical strategy system for building complex searches.

The new user interface contains many new features including:

• A new search strategy interface that enables users to more easily construct complex searches.
• 'User Comments' have been updated to enable submission of supporting evidence including pubmed identifiers and images (or other files). Comments may be added to any gene or sequence page, enhancing available annotation.
• Files can now be uploaded and provided to the community via the file repository section.

New and updated Data:

• P. falciparum reannotation integrated as the official annotation in PlasmoDB (See news item dated 1 February 2008 for details on the reannotation effort).
• P. falciparum High density genotyping array (HD Array) from the Broad Institute (Unpublished).
• P. vivax intraerythrocytic microarray life-cycle (Bozdech et. al.).
• P. vivax microarray from patient samples (Westenberger and Winzeler, unpublished).
• P. chabaudi new 8X assembly and reannotation (Pathogen Sequencing Unit at the Wellcome Trust Sanger Institute, unpublished).
• P. yoelii published gene calls appear as provisional genes in the genome browser (Vaughan et. al.).
• P. yoelii oocyst and salivary gland microarray data (Zhou et. al.).
• Isolate data from GenBank is now integrated and searchable.

Additional features:

• Linkouts are now provided from genes with mutant information in the Genetically Modified Rodent Malaria Parasites database.
• Linkouts are provided to Gene Ontology annotation predictions at Plasmodraft. (Bréhélin et. al.).

  The previous version of PlasmoDB may still be accessed here.