PATRIC December 2010 Release Offers Scores of New and Improved Website Features and Data¶
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¶
Improvements to Genome Overview and Genome List pages to show complete, whole genome sequence (WGS) and plasmid genomes. For respective examples, see http://patricbrc.org/portal/portal/patric/Taxon?cType=taxon&cId=234 and http://patricbrc.org/portal/portal/patric/GenomeList?cType=taxon&cId=234
View and download genomic sequence data directly from the Genome Browser. For example, see http://patricbrc.org/portal/portal/patric/GenomeBrowser?cType=genome&cId=38055&loc=0..10000&tracks=DNA,CDS(PATRIC),gene(PATRIC),RNA(PATRIC)#
Database Cross-References (DBXrefs) from major external databases using UniProt’s IDMapping data are now available on all Feature Overview Pages. For an example, see http://patricbrc.org/portal/portal/patric/Feature?cType=feature&cId=17821513
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
GO Search¶
PATRIC now supports searching based on Enzyme Commission number (EC number); a numerical classification scheme for enzymes that is based on the chemical reactions they catalyze. This new tool allows users to enter a keyword, a known EC number, or a recognized EC name and view all related proteins with that specific annotation.
To view, see http://patricbrc.org/portal/portal/patric/GOSearch?cType=taxon&cId=&dm=
EC Search¶
Similarly, our GO Search allows users to search for proteins based on Gene Ontology (GO) terms representing gene product properties. Users enter a keyword, a known GO term number, or a recognized GO name to view all proteins with that specific annotation.
To view, see http://patricbrc.org/portal/portal/patric/ECSearch?cType=taxon&cId=&dm=
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.