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

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dc.contributor.authorWattam, Alice R.en
dc.contributor.authorDavis, James J.en
dc.contributor.authorAssaf, Ridaen
dc.contributor.authorBoisvert, Sebastienen
dc.contributor.authorBrettin, Thomasen
dc.contributor.authorBun, Christopheren
dc.contributor.authorConrad, Nealen
dc.contributor.authorDietrich, Emily M.en
dc.contributor.authorDisz, Terry L.en
dc.contributor.authorGabbard, Joseph L.en
dc.contributor.authorGerdes, Svetlanaen
dc.contributor.authorHenry, Christopher S.en
dc.contributor.authorKenyon, Ronald W.en
dc.contributor.authorMachi, Dustinen
dc.contributor.authorMao, Chunhongen
dc.contributor.authorNordberg, Eric K.en
dc.contributor.authorOlsen, Gary J.en
dc.contributor.authorMurphy-Olson, Daniel E.en
dc.contributor.authorOlson, Robert D.en
dc.contributor.authorOverbeek, Rossen
dc.contributor.authorParrello, Bruceen
dc.contributor.authorPusch, Gordon D.en
dc.contributor.authorShukla, Mauliken
dc.contributor.authorVonstein, Veronikaen
dc.contributor.authorWarren, Andrew S.en
dc.contributor.authorXia, Fangfangen
dc.contributor.authorYoo, Hyunseungen
dc.contributor.authorStevens, Rick L.en
dc.contributor.departmentFralin Life Sciences Instituteen
dc.contributor.departmentIndustrial and Systems Engineeringen
dc.date.accessioned2019-04-11T18:07:53Zen
dc.date.available2019-04-11T18:07:53Zen
dc.date.issued2017-01-04en
dc.description.abstractThe 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.en
dc.description.notesPATRIC has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services [HHSN272201400027C]. Funding for open access charge: Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services [HHSN272201400027C].en
dc.description.sponsorshipNational Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services [HHSN272201400027C]en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1093/nar/gkw1017en
dc.identifier.eissn1362-4962en
dc.identifier.issn0305-1048en
dc.identifier.issueD1en
dc.identifier.pmid27899627en
dc.identifier.urihttp://hdl.handle.net/10919/88888en
dc.identifier.volume45en
dc.language.isoenen
dc.rightsCreative Commons CC0 1.0 Universal Public Domain Dedicationen
dc.rights.urihttp://creativecommons.org/publicdomain/zero/1.0/en
dc.subjectread alignmenten
dc.subjectgenomeen
dc.subjectannotationen
dc.subjectrasten
dc.subjectassembliesen
dc.subjectalgorithmen
dc.subjectarchiveen
dc.subjectvelveten
dc.subjectgeneen
dc.titleImprovements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Centeren
dc.title.serialNucleic Acids Researchen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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Destination Area: Data and Decisions (D&D)
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