This is the place for the more detailed information.
What
is this feature? PATRIC allows you to annotate your own bacterial
genome for free without leaving the PATRIC website, using the same RAST
annotation service that is used to annotate all other bacterial genomes
available at PATRIC.
How
can you use this feature? In the 'Searches & Tools' drop-down
menu found site-wide at the top of every PATRIC page, choose
'RAST', log in (at the bottom of the page), and submit your genome (
http://patricbrc.vbi.vt.edu/portal/portal/patric/RAST). Within 12 to
24 hours, you will receive an email notification that your annotations are
available. You can review these annotations and/or download them via PATRIC
by again going to 'RAST', logging in, and viewing the results.
What
is this feature? PATRIC allows you to compare protein families, for example, across
diverse groups of genomes, as well as those that are closely related.Comparing proteins that have all been
annotated using the same service (i.e., PATRIC's RAST) eliminates some of the
discrepancy that may be found using other protein family comparison methods.You can also use PATRIC's 'heatmap' viewer
to clearly visualize, for example, shared and unique proteins per family in a
genome.
How
can you use this feature? Protein families are sorted and provided at the genus level via the
'Protein Families' tab. If you
want to compare protein families across genera you can access the 'Protein
Family Sorter' on PATRIC's home page or in the 'Searches and Tools' drop-down menu
found site-wide at the top of
every PATRIC page (http://patricbrc.vbi.vt.edu/portal/portal/patric/FIGfamSorter).
You can choose different groups
using the taxonomy tree, or look alphabetically for genomes of interest. Using the 'Protein Family Sorter' (http://patricbrc.org/portal/portal/patric/FIGfamSorterB?cType=taxon&cId=1279&dm=result),
the comparative possibilities are endless; you can compare protein families
across all pathogenic bacteria, all vaccine strains, all plant symbiotic
bacteria, or make comparisons between pathogenic and symbiotic members, just to
name a few examples.Imagine
assembling core proteins not just at a genus level, but across all
pathogens.
Once you have specified a set of
bacterial genomes of interest, you will see a list of related protein families
and their summary information. Click on a single protein family (in the 'Product Description' column) to
see details for each protein in the family.When viewing a single protein family, you can also generate
a multiple sequence alignment and a phylogenetic tree that represent that
individual family.Clicking under 'Integrated
Protein Tree and Alignment' in the upper right will give you both the tree and corresponding
alignment for all members.To see
an alignment for a subset of members, click appropriate boxes to the left of each
member's 'Genome Name and then choose 'MSA Tool' in the blue bar above the
table.As with all PATRIC tables,
you can download all data in Excel or text format.
On the page listing related
protein families, by selecting the 'Heatmap' tab (to the right of the 'Table'
tab above the table), you can get a visual indication of the number of
individual proteins per genome in that family (http://patricbrc.org/portal/portal/patric/FIGfamSorterB?cType=taxon&cId=1637&dm=result#gs_0=-1757147348).From PATRIC's heatmap viewer, you can
drag the cursor over protein families of interest, click to select them, and
download all corresponding information.
Screen
from PATRIC Protein Heatmap:
What
is this feature? You can BLAST any user-provided nucleotide or amino acid sequence of
interest against PATRIC's plasmids using common
variants of NCBI's BLAST. This feature is particularly useful if you are interested in
horizontal transfer.
How
can you use this feature? In the 'Searches & Tools' drop-down menu found site-wide
at the top of every PATRIC page,
choose BLAST (
http://patricbrc.vbi.vt.edu/portal/portal/patric/Blast?dm=result&pk=-1084078847) to view a page
providing a suite of BLAST-related options and controls. To specify a BLAST against plasmid
sequences, select the drop-down menu labeled 'Database' (to the left of the
menu) to view the variety of databases to BLAST against. Then from the menu select 'Plasmid
sequences' to BLAST against genomic sequences, 'PATRIC protein (plasmid)' to
BLAST against plasmid proteins annotated by RAST, or 'RefSeq
protein (plasmid)' to BLAST against plasmid annotations available at RefSeq.
What
is this feature? Researchers often gain insight by viewing pathways in which their particular
protein of interest is involved.PATRIC maps all its proteins to KEGG pathways.Some genes are involved in multiple pathways, and KEGG
pathway names are provided.There
are sometimes surprising differences in EC annotations from other annotation
sources, which highlights the utility of being able to compare different types
of annotation.
Pathways are also available in
PATRIC at any taxonomic level, not just gene or protein level.Simply start at the taxonomic level of
interest and choose the tab labeled 'Pathways'.This will display a table that lists all KEGG pathways
annotated for that taxonomic level(
http://patricbrc.org/portal/portal/patric/CompPathwayMap?cType=genome&cId=38055&map=00010&algorithm=PATRIC).
Different
tabs at the top of this table let you see 'Pathways', 'EC numbers', and 'Genes'
that have been annotated. Clicking
on 'Pathway Name' displays a KEGG pathway map, to the left of which is a
summary table of 'EC number', 'Genome count', 'Feature count', 'Genome count',
and 'Occurrence'.These EC numbers
are present in genomes at this taxonomic level.Clicking on an
EC number in the table highlights in red the corresponding EC number in the
KEGG pathway map.Also, a
'Heatmap' tab at the top left of the KEGG pathway table provides a visual
presentation of EC number representation by genome.
Screen
from PATRIC Comparative Pathways Map:
What
is this feature? PATRIC not only consistently annotates all genomes using the RAST
system, but also stores and displays annotations from other resources, notably
RefSeq and the former Biological Resource Centers (BRCs), like ERIC and
PATHEMA.These are called 'Legacy
BRC' at PATRIC.This is a unique
and notable difference between PATRIC and other bacterial websites, where only
one flavor of annotation is available.Sometimes the differences are surprising, so it is important to be able
to make comparisons.
How
can you use this feature? You can access and compare annotations from different resources in
various ways.On the home
page at any taxonomic level, you can choose the 'Feature Table'.The default, immediately visible, lists
features annotated by PATRIC.The 'Annotation'
drop-down menu allows you to choose one available type of annotation, or you
can choose 'All'.
Another way to visualize the
differences in annotation is by using PATRIC's Genome Browser.If you are interested in a particular feature
in the table, you can click on the Genome Browser icon located to the right of
the 'Locus Tag'.This will bring
up PATRIC's Genome Browser (http://patricbrc.org/portal/portal/patric/GenomeBrowser?cType=genome&cId=78565&loc=0..10000&tracks=DNA,CDS(PATRIC),gene(PATRIC),RNA(PATRIC)
), and the default setting is for PATRIC annotation.To add tracks (annotations) from other annotation sources,
choose one of the boxes along the left side and drag it into the desired main Browser
area.
You can also access PATRIC's
Genome Browser at some other taxonomic levels.For example, at any genome home page, you can browse an
entire chromosome by choosing the Genome Browser symbol within the 'Sequence
Summary' box at the top of the page.You can also access it from any 'Genome List' tab.Once again, the default is features
annotated by PATRIC; you can drag and drop any annotations/feature types you wish
to see from other sources.
Screen
from PATRIC Comparative Genome Browser:
What is this feature?
The VectorBase Expression Browser contains
high quality curated expression data from a wide
range of microarray experiments performed on vector species. For each
gene or microarray probe a short statistical summary of the experimental
results is shown along with other information integrated with the VectorBase Genome Browser.
How can you use this feature?
Access our expression browser at http://funcgen.vectorbase.org/ExpressionData/
where summary pages, plots and tables of data are available to view or
download. Sequencing-based expression studies will also be incorporated
as they become available. The precise location of microarray probes on
the genome may also be visualized in the Genome Browser.
What is this feature?
You can find terms, their definitions and
images (when applicable) for multiple ontologiescurated by VectorBase staff via a
searchable interface.
How can you use this feature?
When you perform a query in an ontology-based
database you can find terms, their definitions and images in the CV search
section.This can be expanded
to include all children of the original query term.For example, if at any point when you are looking
at the insecticide resistance data in VectorBase you
are not certain about a specific term, you can search for a
more generic term and drill down in the ontology. All relevant results
will then be displayed in our custom user interface.
What is this feature?
All news stories about the data, tools relevant
to your research, jobs, and meetings that VectorBase
staff will attend will automatically populate your favorite news
application as our team posts them.
How can you use this feature?
Subscribe by clicking the 'RSS Feed' link
at the bottom of the VectorBase home page and
following the instructions on your web browser.You are also welcome to follow VectorBase
on FaceBook and twitter if you prefer these streams
of news content.
What is this feature?
The BioMart interface allows complex queries on three VectorBase data sets
(genes, expression, and variations) without having to know the underlying
structure of VectorBase data.
How can you use this feature?
Follow the 'BioMart' link in the 'Retrieve Data' section on the home page. A
drop-down menu will let you to select a data type (gene, expression,
and variation) and a species. Choose the appropriate 'Filters' to restrict
your query to specific fields and select 'Attributes' to add in your desired
output. Note that BioMart is also accessible programmatically for advanced
users.
What is this feature?
VectorBase compares the proteomes of its species of interest; a list of
orthologs and paralogs between two given species is generated automatically
every gene build release.
How can you use this feature?
It is accessible in the Genome Browser, from the left hand menu in a 'gene'
tab, under 'Comparative Genomics'. Results are available as an image with
collapsible/expandable taxonomic categories, as text in Newick format, or
as a multiple alignment of all proteins in the tree.
What
is this feature?
Display
location of mature peptide in the genome and the polyprotein
View the
mature peptide's annotation, isoelectric point, molecular weight,
domains/motifs, epitopes, similar proteins based on blastp results, and
more.
2.From the 'Search Data' tab, click on 'Gene/Protein Search'.
3.Search
gene/protein by virus, gene symbol, gene name, genomic location, or public
database identifier.
4.On the search
result page, click on to view
details about a protein.
5.On the Protein/Gene Details page, you can view
the protein's location in the genome image map, as well as the protein's
annotation, isoelectric point, molecular weight, domains/motifs, epitopes,
similar proteins based on blastp results, and more.
What
is this feature?
Align
multiple virus sequences
Visualize
alignments with derived consensus sequence and conservation score
2.From the 'Search Data' tab, click on '3D Protein Structures'.
3.Search
protein structures by virus, keyword, author, public database identifier,
etc.
4.From the
search result list, click on 'View
Structure' to access the structure viewer page.
5.You can
choose to highlight ligands, epitopes, and residues when available on your
protein structure.
6.Download your
highlighted protein structure image by clicking on 'Save View As Image'.
What
is this feature? The
ViPR Workbench provides free online storage space for you to:
Save and
organize working sets of sequences, analysis results and search criteria
Share
working sets and analysis results with others
Upload
personal sequences and combine with existing working sets
How can you use this feature?
•Register for a workbench with ViPR: On the ViPR homepage (http://www.viprbrc.org/brc/home.do?decorator=vipr), click on 'Save
to Workbench – Sign up!'
and follow the instruction there; from the blue banner at the top of any
individual virus webpage, click on 'Workbench Sign In' or the grey 'Workbench' tab
to register an account with ViPR using your email address and a password.
•To save sequences or
other data, click on on the search result page and
follow the instruction there.
•To save searches, after you run a search,look for on the search result page and save the search to your
workbench; or, go to 'Search Data – YourSearch History' or your workbench, select the search you want to save and click on 'Save'.
•To
save analysis results, after you run an analysis,
look for on the
analysis result page and save the analysis to your workbench; or, go to 'Analyze & Visualize –YourAnalysis History' or your workbench, select the analysis you want to
save and click on 'Save'.
•To
share working sets and analysis results, select items in your workbench that you want
to share,then click on the 'Sharing' tab and
follow the instruction there.
•To upload your
personal sequences, log
in to your workbench, click on 'More Actions – Upload File'
and follow the instruction there.
What
is this feature?
•Search avian
and other surveillance data by subtype, geographic locations and various host
characteristics
Display
data on a map, color code by flu prevalence, and overlay with bird migration
flyways
Create
customized report showing surveillance records grouped by characteristics
of your choice
2.Upload/paste
your own sequences or use working set that you have saved to your Workbench.
3.Select 'Output Format' and 'Output Order' and run analysis.
4.On the
Alignment Report page, hover over the tab
and click on 'Visualize Aligned
Sequences' or 'Generate
Phylogenetic Tree' depending on your purpose.
5.You can
customize the label on your alignment result or on your phylogenetic tree.
6.On the
Alignment Report page, click on to save the alignment to your IRD
Workbench.
What
is this feature?
Visualize
protein 3D structures in various display formats
Display
sequence conservation heat map on the structure
Highlight
ligands, epitopes, sequence features and more on the structure
Download
protein structure image with highlighted residues
2.Search
protein structures by virus type, strain name, protein, protein structure
highlight feature, keyword, author, public database identifier, etc.
3.From the search
result list, click on 'View Structure'
to access the structure viewer page.
4.You can
choose to highlight sequence conservation, ligands, epitopes, residues, and
sequence features when available on your protein structure.
5.Download your highlighted protein structure
image by clicking on 'Save View As
Image'.
What
is this feature? The
IRD Workbench provides free online storage space for you to:
Save and
organize working sets of sequences, analysis results and search criteria
Share
working sets and analysis results with others
Upload
personal sequences and combine with existing working sets
•To save sequences or other data, click on on the search result page and
follow the instruction there.
•To
save searches, after you run a search,look for on the search result page and save the
search to your workbench; or,
go to 'Search Data – YourSearch History' or your workbench, select the search you want to
save and click on 'Save'.
•To
save analysis results, after you run an
analysis, look for on the
analysis result page and save the analysis to your workbench; or, go to 'Analyze & Visualize –YourAnalysis History' or your workbench, select the analysis you want to
save and click on 'Save'.
•
To
share working sets and analysis results, select items in your workbench that you want to share,then click on the 'Sharing' tab and
follow the instruction there.
• To upload
your personal sequences, log in to your workbench, click on 'More
Actions – Upload File' and follow the instruction there.
