Now showing items 1-6 of 6

    • Antimicrobial Resistance Prediction in PATRIC and RAST 

      Davis, James J.; Boisvert, Sebastien; Brettin, Thomas; Kenyon, Ronald W.; Mao, Chunhong; Olson, Robert; Overbeek, Ross; Santerre, John; Shukla, Maulik; Wattam, Alice R.; Will, Rebecca; Xia, Fangfang; Stevens, Rick (Springer Nature, 2016-06-14)
      The emergence and spread of antimicrobial resistance (AMR) mechanisms in bacterial pathogens, coupled with the dwindling number of effective antibiotics, has created a global health crisis. Being able to identify the genetic ...
    • Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center 

      Wattam, Alice R.; Davis, James J.; Assaf, Rida; Boisvert, Sebastien; Brettin, Thomas; Bun, Christopher; Conrad, Neal; Dietrich, Emily M.; Disz, Terry; 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; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Vonstein, Veronika; Warren, Andrew; Xia, Fangfang; Yoo, Hyunseung; Stevens, Rick L. (2017-01-04)
      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 ...
    • PATRIC, the bacterial bioinformatics database and analysis resource 

      Wattam, Alice R.; Abraham, David; Dalay, Oral; Disz, Terry L.; Driscoll, Timothy; Gabbard, Joseph L.; Gillespie, Joseph J.; Gough, Roger; Hix, Deborah; Kenyon, Ronald; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K.; Olson, Robert; Overbeek, Ross; Pusch, Gordon D.; Shukla, Maulik; Schulman, Julie; Stevens, Rick L.; Sullivan, Daniel E.; Vonstein, Veronika; Warren, Andrew; Will, Rebecca; Wilson, Meredith J. C.; Yoo, Hyun Seung; Zhang, Chengdong; Zhang, Yan; Sobral, Bruno W. (2014-01)
      The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious ...
    • PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database 

      Davis, James J.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Pusch, Gordon D.; Shukla, Maulik; Vonstein, Veronika; Wattam, Alice R.; Yoo, Hyunseung (Frontiers, 2016-02-08)
      The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation, and metabolic modeling. For several years we have been maintaining protein ...
    • RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes 

      Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Thomason, James A., III; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang (Springer Nature, 2015-02-10)
      The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features ...
    • The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) 

      Overbeek, Ross; Olson, Robert; Pusch, Gordon D.; Olsen, Gary J.; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Parrello, Bruce; Shukla, Maulik; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang; Stevens, Rick (2014-01)
      In 2004, the SEED (http://pubseed.theseed.org/) was created to provide consistent and accurate genome annotations across thousands of genomes and as a platform for discovering and developing de novo annotations. The SEED ...