PATRIC December 2010 Release Offers Scores of New and Improved Website Features and Data

Published on 2010-12-10

Website Enhancements

New Virulence and Disease Information

Information related to virulence, disease and outbreaks is now available through a new PATRIC tab at all taxonomy levels.

  • Shows relationship between pathogens, diseases, virulence factors, and host genes.
  • Represents data in tables, as well as, in a graph visualization.
  • Includes global disease reports (e.g., incidents and other) in an interactive map as provided in collaboration with Health Map.

For an example, see http://patricbrc.org/portal/portal/patric/DiseaseOverview?cType=taxon&cId=1763

New Phylogenetic/Species Tree Viewer

We have updated all PATRIC phylogenetic trees to include latest genomes.  These are accessed via a our new interactive, multicolor tree viewer which show large trees and phylogenetic relationships more efficiently and effectively than traditional coloring schemes.

For an example, see http://patricbrc.org/portal/portal/patric/Phylogeny?cType=taxon&cId=356

Improved Protein Family Sorter

The Protein Family Sorter (PFS) is now available as a tab from taxonomy pages at genus level and below.  PFS now includes:

  • PATRIC’s Protein Family Sorter allows users to search and filter on FIGfams and now provides improved coverage (as compared to previous releases) of proteins in PATRIC.
  • New interactive heatmap visualization that allows users to visually sift through large numbers of protein families based on their presence or absence in the genomes of interest. Users can select collections of proteins (from genomes and/or protein families of interest) from the heatmap and download related data in multiple formats.  For an example, see http://test.patricbrc.org/portal/portal/patric/FIGfamSorterB?cType=taxon&cId=1392&dm=result#gs_0=-1638842268.
  • New interactive multiple sequence alignment (MSA) for protein families.   More information on MSA is described below.

For an example, see http://patricbrc.org/portal/portal/patric/FIGfamSorter?cType=taxon&cId=234&dm=result

Protein Structure Viewer

To support exploration of protein structures, PATRIC now boasts an interactive JMOL-based viewer that displays 3D protein structures (accessible via the ‘Experiment Data’ tab at all taxon levels). Features, such as ligands, chains, and secondary structure annotations, can be dynamically displayed directly on these structures using interactive controls.

For an example of a structure list, see http://patricbrc.org/portal/portal/patric/Structure?cType=taxon&cId=234&filter=ssgcid#key=1747&pS=20&aP=1

For an example of our 3D viewer, see http://patricbrc.org/portal/portal/patric/Jmol?structureID=3P0X

Integration with BEIResources and Structural Genomics Centers

We now offer direct links from specific PATRIC structures to clone sets available from Biodefense & Emerging Infections Research Resources Repository (BEIRRR).  Specifically, PATRIC links to BEIRRR clones which were submitted by the Seattle Structural Genomics Center for Infectious Disease (SSGCID) and the Center for Structural Genomics of Infectious Diseases (CSGID).  These links are available from appropriate feature and structure pages.

New Interactive Multiple Sequence Alignment Viewer Now Available from Protein Family Sorter

PATRIC’s new multiple sequence alignment (MSA) viewer displays MSA and family tree side-by-side and allows users to collapse/expand tree branches in order to co-locate sequences of interest.  The MSA viewer also allows interactive coloring of amino acids in the MSA based on conservation per position.


Enhanced Genome Selector in all Searches and Tools

Many of PATRIC’s searches and tools allow users to select specific orders, species, etc. in order to scope their search accordingly.  To improve the selection process across all of these searches and tools, PATRIC now provides an improved genome selection panel that allows on-the-fly, in-line search to quickly find taxonomy nodes or genomes of interest.  Searching and selecting is supported in the (previously released) taxonomy tree structure, as well as, the new alphabetized list.

For an example of the enhanced genome selector, see http://patricbrc.org/portal/portal/patric/GenomeFinder?cType=taxon&cId=&dm=

Improved Toolbar for All PATRIC Tables

Every table in PATRIC (e.g., feature tables, search result tables, tables of protein families), now sport an Improved toolbar design with intuitive icons and grouping of related actions.   These new table toolbars allow users to select items in the table and perform various actions on them, such as view sequence data, download data, send selected features to analysis tools (e.g., MSA), and so on.

For an example, see http://patricbrc.org/portal/portal/patric/FeatureTable?cType=taxon&cId=234

PATRIC Group Explorer

Throughout the site, users can create custom ad-hoc groups of features using PATRIC’s ‘Add to Cart’ button on any table’s control bar.  Once groups have been created, users can employ the Group Explorer to compare, contrast and even crate new groups using a Venn diagram-based interactive visualization.  Users’ can conveniently access the Group Explorer from the Feature Cart icon at the top of every PATRIC page.

For more information, see the PATRIC Group Explorer FAQs.

Improved Protein Family Sorter

The Protein Family Sorter (PFS) is now available as a tab from taxonomy pages at genus level and below.  PFS now includes:

  • PATRIC’s Protein Family Sorter allows users to search and filter on FIGfams and now provides improved coverage (as compared to previous releases) of proteins in PATRIC.
  • New interactive heatmap visualization that allows users to visually sift through large numbers of protein families based on their presence or absence in the genomes of interest. Users can select collections of proteins (from genomes and/or protein families of interest) from the heatmap and download related data in multiple formats.  For an example, see http://test.patricbrc.org/portal/portal/patric/FIGfamSorterB?cType=taxon&cId=1392&dm=result#gs_0=-1638842268.
  • New interactive multiple sequence alignment (MSA) for protein families.   More information on MSA is described below.

For an example, see http://patricbrc.org/portal/portal/patric/FIGfamSorter?cType=taxon&cId=234&dm=result

Subscribe to PATRIC Newsletters

PATRIC is now encouraging users to sign up to receive quarterly newsletters.  Newsletters will be used to announce new PATRIC data, tools, website features, and events.  Recipients will also receive PATRIC-funded requests for proposals.  To subscribe, use PATRIC’s new ‘Subscribe’ link located at the top of every PATRIC page, or use the subscription form on our PATRIC Facebook page.

PATRIC is Now on Facebook and YouTube

PATRIC now has a social media presence at both Facebook and YouTube. Our Facebook page shows our latest news and allows Facebook users to share PATRIC’s resrouces with their colleagues.  PATRIC’s YouTube page, is newly established, but will contain short videos that describe PATRIC website features, as well as, videos of appropriate workshop content.

Miscellaneous Enhancements to the PATRIC Website

New Searches and Tools

Plasmid BLAST

PATRIC now supports plasmid-specific BLAST databases containing genomic sequences and proteins (annotated by PATRIC and RefSeq) from all of the plasmids in PATRIC database.  As such, users can BLAST PATRIC or custom sequences specifically against all PATRIC bacterial plasmids.  To view, see http://patricbrc.org/portal/portal/patric/Blast

Data Download Tool

****The new Download Tool allows users to select multiple genomes and download corresponding annotations in various different file formats in a single click. ****To view, see http://patricbrc.org/portal/portal/patric/Downloads

MG-RAST

We now provide an interface to the metagenome RAST annotation service (MG-RAST).

To view, see http://patricbrc.org/portal/portal/patric/MGRAST

Genomes and Annotations

In this release, 322 new genomes have been added and annotated by RAST since PATRIC’s August 2010 release.  The following table summarizes the data available in the PATRIC database through December, 2010 PATRIC Website Release.

PATRIC

Legacy BRC

RefSeq

Number of genomes

2548

405

2939

Number of complete genomes

1241

251

1227

Number of WGS genomes

1307

149

1332

Number of Plasmid only genomes

5

380

For summary, see http://patricbrc.org/portal/portal/patric/Taxon?cType=taxon&cId=2

Annotations Updates & Synchronization

Functional annotation of all the proteins (i.e. product, GO, EC, and pathway assignments) have been updated based on the latest FIGFams. Functional annotations are now consistent across all genomes in the PATRIC database.