Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

Date
2017-01-04Author
Wattam, Alice R.
Davis, James J.
Assaf, Rida
Boisvert, Sebastien
Brettin, Thomas
Bun, Christopher
Conrad, Neal
Dietrich, Emily M.
Disz, Terry L.
Gabbard, Joseph L.
Gerdes, Svetlana
Henry, Christopher S.
Kenyon, Ronald W.
Machi, Dustin
Mao, Chunhong
Nordberg, Eric K.
Olsen, Gary J.
Murphy-Olson, Daniel E.
Olson, Robert D.
Overbeek, Ross
Parrello, Bruce
Pusch, Gordon D.
Shukla, Maulik
Vonstein, Veronika
Warren, Andrew S.
Xia, Fangfang
Yoo, Hyunseung
Stevens, Rick L.
Metadata
Show full item recordAbstract
The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user- created genome-groups, with detailed summaries and views of the data that researchers have selected. Perhaps the biggest change has been the enhanced capability for researchers to analyze their private data and compare it to the available public data. Researchers can assemble their raw sequence reads and annotate the contigs using RASTtk. PATRIC also provides services for RNA-Seq, variation, model reconstruction and differential expression analysis, all delivered through an updated private workspace. Private data can be compared by `virtual integration' to any of PATRIC's public data. The number of genomes available for comparison in PATRIC has expanded to over 80 000, with a special emphasis on genomes with antimicrobial resistance data. PATRIC uses this data to improve both subsystem annotation and k-mer classification, and tags new genomes as having signatures that indicate susceptibility or resistance to specific antibiotics.