Genomes are received on a regular basis from a multitude of sources (GenBank, RefSeq, Collaborator Request, etc.). Our signature PATRIC annotation is generated via the RAST (Rapid Annotation Subsystems Technologies) Pipeline, resulting in a consistently annotated set of genomes in which meaningful comparisons can be made within and across taxonomic boundaries. We also maintain the original annotations from GenBank to allow users to explore and compare annotation differences. In addition, we automatically gather, parse, and curate over 60 various associated metadata attributes, such as isolation source, geographic location, and host. Find out how to search for genomes of interest in our Genome Finder FAQs.
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Data in PATRIC is organized in a similar fashion at various taxonomic levels throughout the website.Â Follow along in this Mycobacterium example and see what data is available and where to find it for your favorite organisms/genomes/genes.
This downloadable pdf contains screenshots and detailed step-wise instructions for locating data of interest, such as finding a particular gene, finding the pan-proteome for all Mycobacterium genomes using the Protein Family Sorter and Heatmap, and examining pathways across Mycobacterium using the Comparative Pathway Tool and Heatmap.
Between the spring of 2011 and June of 2012, twenty-seven new E. coli genomes were sequenced as a result of a European E. coli outbreak. Learn how we identify areas of these genomes that are different (e.g., missing or unique proteins) when compared to their closest phylogenetically-related E. coli genomes and then search for evidence of lateral transfer in cases where unique proteins were found in new virulent strains.
Find out more about PATRIC data, analysis tools, and functionality in our Frequently Asked Questions.
As a result of the foodborne illness outbreak in Europe in 2011, numerous new E. coli genomes were sequenced and found to have acquired the genes necessary to produce Shiga toxins, which are believed to play a role in the strains’ high virulence. See how to identify and collect these genomes and the full set of Shiga toxins associated with them for further analysis.
See how to use PATRIC tables and the Table Toolbar including sorting, downloading, analysis tools, creating persistent column customization, and saving items to your workspace.
This downloadable pdf contains screenshots and detailed step-wise instructions for locating data of interest, such as finding a particular gene, finding the pan-proteome for all Brucella genomes using the Protein Family Sorter and Heatmap, and examining pathways across Brucella using the Comparative Pathway Tool and Heatmap.