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dc.contributor.authorWattam, Alice R.
dc.contributor.authorDavis, James J.
dc.contributor.authorAssaf, Rida
dc.contributor.authorBoisvert, Sebastien
dc.contributor.authorBrettin, Thomas
dc.contributor.authorBun, Christopher
dc.contributor.authorConrad, Neal
dc.contributor.authorDietrich, Emily M.
dc.contributor.authorDisz, Terry
dc.contributor.authorGabbard, Joseph L.
dc.contributor.authorGerdes, Svetlana
dc.contributor.authorHenry, Christopher S.
dc.contributor.authorKenyon, Ronald W.
dc.contributor.authorMachi, Dustin
dc.contributor.authorMao, Chunhong
dc.contributor.authorNordberg, Eric K.
dc.contributor.authorOlsen, Gary J.
dc.contributor.authorMurphy-Olson, Daniel E.
dc.contributor.authorOlson, Robert
dc.contributor.authorOverbeek, Ross
dc.contributor.authorParrello, Bruce
dc.contributor.authorPusch, Gordon D.
dc.contributor.authorShukla, Maulik
dc.contributor.authorVonstein, Veronika
dc.contributor.authorWarren, Andrew
dc.contributor.authorXia, Fangfang
dc.contributor.authorYoo, Hyunseung
dc.contributor.authorStevens, Rick L.
dc.date.accessioned2019-04-11T18:07:53Z
dc.date.available2019-04-11T18:07:53Z
dc.date.issued2017-01-04
dc.identifier.issn0305-1048
dc.identifier.urihttp://hdl.handle.net/10919/88888
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_US
dc.description.sponsorshipNational Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services [HHSN272201400027C]
dc.format.mimetypeapplication/pdf
dc.language.isoen_US
dc.rightsCC0 1.0 Universal
dc.rights.urihttp://creativecommons.org/publicdomain/zero/1.0/
dc.subjectread alignment
dc.subjectgenome
dc.subjectannotation
dc.subjectrast
dc.subjectassemblies
dc.subjectalgorithm
dc.subjectarchive
dc.subjectvelvet
dc.subjectgene
dc.titleImprovements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Centeren_US
dc.typeArticle - Refereed
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].
dc.title.serialNucleic Acids Research
dc.identifier.doihttps://doi.org/10.1093/nar/gkw1017
dc.identifier.volume45
dc.identifier.issueD1
dc.type.dcmitypeText
dc.identifier.pmid27899627
dc.identifier.eissn1362-4962


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