A list of all proteins and their conformity scores is provided in an Excel file (ecoli9genocav).  Some of the proteins found in the outbreak strains have no homologs in E. coli.  In the conformity score column, these “unique” proteins are identified by a “-“.  The data for the unique proteins for all nine strains are also integrated into the PATRIC website, with the additional functionality the site provides (where applicable); you can access those data at the following links:

• LB226692 unique genes
• TY-2482 unique genes
• GOS1 unique genes
• GOS2 unique genes
• H112180280 unique genes
• H112180282 unique genes
• H112180283 unique genes
• H112180540 unique genes
• H112180541 unique genes

The divergent proteins (see above) were compared to virulence and antibiotic-resistance proteins collected from different sources with some interesting discoveries.  For example, beta-lactamase, a protein responsible for resistance to beta-lactam antibiotics like penicillins, cephamycins, and carbapenems was found to be identical in the nine outbreak strains (CTX-M type), but very different from their closest homologs prevalent in other E. coli strains (TEM-type).  An alignment of these proteins is shown here.  Other divergent proteins include ABC transporters, phage-related and outer-membrane proteins.

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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:

Course Authors: Joseph L. Gabbard (Virginia Tech), J. Edward Swan II (Mississippi State University) & Chris North (Virgina Tech)

Course Description: This tutorial is for researchers and engineers, working in the field of visualization, who wish to conduct user-based visualization experiments with a specific aim of promoting both traditional quantitative human-subject experiments and qualitative methods for assessing usability and insight. This tutorial presents both quantitative and qualitative approaches to human-subject experiments of visualizations. It covers (1) the basic principles of experimental design and analysis, with an emphasis on human-subject experiments in visualization; (2) formative evaluation methods for iteratively assessing and improving visualization user interfaces; and (3) approaches to designing and conducting qualitative studies that aim to measure the degree to which specific visualization designs afford insight formation.

Who should attend: Researchers and engineers, working in the visualization fields (Vis, InfoVis, VAST, BioVis), who wish to either (1) conduct evaluation experiments with human subjects, and / or (2) gain a better understanding of the basic terminology of experimental design and analysis (e.g., the precise meaning of statements such as [F(2,45) = 5.67, p = .023]), and / or (3) are researching or developing visualizations that can benefit from qualitative user-based assessment (e.g., visualizations that are at or beyond prototyping phases and are readying for potential broader use). Level of expertise: All Levels. This material is useful to attendees with multiple levels of expertise.

Read full article on RAST German E. coli Strain Annotation Using Cloud Computing.

The seminar was held at Virginia Bioinformatics Institute in conjunction with the Genetics, Bioinformatics, and Computational Biology (GBCB) Seminar Series.  An associated hands-on workshop followed.  Details below.

What PATRIC Offers:

• Consistent annotations across all sequenced bacterial species from GenBank.

• Searches based on taxonomy, gene name, locus tag, protein function/families, pathways, EC numbers, GO terms, and more.

• Data and analysis results are free and typically downloadable.

• Organism summaries; pre-sorted PubMed articles; interactive phylogenetic trees; virulence and disease information, and experimental data including, transcriptomics, proteomics, protein structure, and protein-protein interactions.

• Numerous interactive visualizations for genome browsing, multi-genome comparisons, pathway comparisons, protein family comparisons, phylogenetic trees with coupled MSAs, 3D protein structures, and feature group comparisons.

Event includes free pizza dinner.  For registration information, agenda, and location details please see PATRIC VT Workshop Flyer.

If you have a suggestion for a future workshop topic and/or location, please send it to us via the “contact us” link at the bottom of this page.

• Consistent annotations across all sequenced bacterial species from GenBank.

• Searches based on taxonomy, gene name, locus tag, protein function/families, pathways, EC numbers, GO terms, and more.

• Data and analysis results are free and typically downloadable.

• Organism summaries; pre-sorted PubMed articles; interactive phylogenetic trees; virulence and disease information, and experimental data including, transcriptomics, proteomics, protein structure, and protein-protein interactions.

• Numerous interactive visualizations for genome browsing, multi-genome comparisons, pathway comparisons, protein family comparisons, phylogenetic trees with coupled MSAs, 3D protein structures, and feature group comparisons.

Event includes free pizza dinner.  For registration information, agenda, and location details please see PATRIC VT Workshop Promo.

If you have a suggestion for a future workshop topic and/or location, please send it to us via the “contact us” link at the bottom of this page.