PATRIC November 2011 Release Highlights New Global Search and Enhanced Personal Workspace

Published on 2011-12-01

Search PATRIC Data Using Single Site-wide Search Box:

  • Every PATRIC page now includes a search box (top right, in the blue banner) that will search across PATRIC data types.
  • Results are presented in a “Google-like” fashion, including a summary view and several data-specific views (e.g., features by function, genomes, etc.).
  • Users can search on locus tags, function names, genome names, and much more.
  • Search results include a collapsible toolbar, allowing the user to select specific search results of interest and perform actions (e.g., view sequence data, add features to workspace, etc.).
  • PATRIC’s existing specialized searches (Feature Finder, GO Term Search, ) are still available from the main “Searches & Tools” navigation menu.

User Workspace Overhaul:

  • This release includes a completely redesigned user workspace that embraces an iTunes-like interface.
  • The user can view groups or lists of workspace items, and filter them based on certain metadata (e.g., group name, tag, etc.).
  • All users (including registered users and guests) can add both features and genomes to workspace, allowing for multiple levels of analysis and comparison.
  • When adding items to the workspace, users can chose whether to group them, or simply tag them for more flexible, ad hoc grouping in the workspace.
  • Registered users’ workspace are persistent, meaning that all their work is saved between working sessions.
  • Genome groups can be used to scope all PATRIC’s advanced Searches and Tools, allowing users to create reusable sets of genomes in which to, for example, explore pathways, browse protein families, and more.

Genomes and Annotations

Since August 2011, 284 new genomes have been added to PATRIC.  In addition, 16 genomes have been updated or replaced with their newest versions.  In total, 279 new genomes have been annotated using RAST.

A summary of the genomes available on the PATRIC website through November, 2011 is provided in the table below:

PATRIC

Legacy BRC

RefSeq

Number of genomes

3807

337

3920

Number of Complete genomes

1619

237

1617

Number of WGS genomes

2188

96

1906

Number of Plasmid only genomes

4

397