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PyCogent: a toolkit for making sense from sequence

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Knight, Rob; Maxwell, Peter; Birmingham, Amanda; Carnes, Jason; Caporaso, J Gregory; Easton, Brett C; Eaton, Michael; Hamady, Micah; Lindsay, Helen; Liu, Zongzhi; Lozupone, Catherine; McDonald, Daniel; Robeson, Michael; Sammut, Raymond; Smit, Sandra; Wakefield, Matthew J; Widmann, Jeremy; Wikman, Shandy; Wilson, Stephanie; Ying, Hua; Huttley, Gavin A

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We have implemented in Python the COmparative GENomic Toolkit, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics. PyCogent includes connectors to remote databases, built-in generalized probabilistic techniques for working with biological sequences, and controllers for third-party applications. The toolkit takes advantage of parallel architectures and runs on a range of...[Show more]

dc.contributor.authorKnight, Rob
dc.contributor.authorMaxwell, Peter
dc.contributor.authorBirmingham, Amanda
dc.contributor.authorCarnes, Jason
dc.contributor.authorCaporaso, J Gregory
dc.contributor.authorEaston, Brett C
dc.contributor.authorEaton, Michael
dc.contributor.authorHamady, Micah
dc.contributor.authorLindsay, Helen
dc.contributor.authorLiu, Zongzhi
dc.contributor.authorLozupone, Catherine
dc.contributor.authorMcDonald, Daniel
dc.contributor.authorRobeson, Michael
dc.contributor.authorSammut, Raymond
dc.contributor.authorSmit, Sandra
dc.contributor.authorWakefield, Matthew J
dc.contributor.authorWidmann, Jeremy
dc.contributor.authorWikman, Shandy
dc.contributor.authorWilson, Stephanie
dc.contributor.authorYing, Hua
dc.contributor.authorHuttley, Gavin A
dc.date.accessioned2016-01-18T02:34:16Z
dc.date.available2016-01-18T02:34:16Z
dc.identifier.issn1465-6906
dc.identifier.urihttp://hdl.handle.net/1885/95500
dc.description.abstractWe have implemented in Python the COmparative GENomic Toolkit, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics. PyCogent includes connectors to remote databases, built-in generalized probabilistic techniques for working with biological sequences, and controllers for third-party applications. The toolkit takes advantage of parallel architectures and runs on a range of hardware and operating systems, and is available under the general public license from http://sourceforge.net/projects/pycogent.
dc.description.sponsorshipThis project used facilities and/or funding provided to GA Huttley by the Australian Partnership for Advanced Computing, Cray Australia Pty. Ltd., the Australian Research Council, the National Health and Medical Research Council, and software licenses donated by Wingware; and funding support provided to R Knight from the Keck RNA Bioinformatics Initiative, Jane and Charlie Butcher Foundation, NIH Signaling and Cellular Regulation Training Grant, NIH Biophysics Training Grant, and the National Academy Keck Futures Initiative.
dc.publisherBioMed Central
dc.rights© 2007 Knight et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.sourceGenome Biology
dc.subjectanimals
dc.subjectbrca1 protein
dc.subjectdatabases, genetic
dc.subjectgenomics
dc.subjecthumans
dc.subjectphylogeny
dc.subjectprotein conformation
dc.subjectproteobacteria
dc.subjectsequence analysis
dc.subjectvon willebrand factor
dc.subjectsoftware
dc.titlePyCogent: a toolkit for making sense from sequence
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume8
dc.date.issued2007-08-21
local.identifier.absfor060407
local.identifier.ariespublicationU1408929xPUB280
local.publisher.urlhttp://www.biomedcentral.com/
local.type.statusPublished Version
local.contributor.affiliationKnight, Rob, University of Colorado, United States of America
local.contributor.affiliationMaxwell, Peter, College of Medicine, Biology and Environment, CMBE John Curtin School of Medical Research, JCSMR General, The Australian National University
local.contributor.affiliationBirmingham, Amanda, Thermo Fisher Scientific, United States of America
local.contributor.affiliationCarnes, Jason, Seattle Biomedical Research Institute, United States of America
local.contributor.affiliationCaporaso, J Gregory, University of Colorado, United States of America
local.contributor.affiliationEaston, Brett, College of Medicine, Biology and Environment, CMBE John Curtin School of Medical Research, JCSMR General, The Australian National University
local.contributor.affiliationEaton, Michael, Science Applications International Corporation, United States of America
local.contributor.affiliationHamady, Micah, University of Colorado, United States of America
local.contributor.affiliationLindsay, Helen, College of Medicine, Biology and Environment, CMBE John Curtin School of Medical Research, JCSMR General, The Australian National University
local.contributor.affiliationLiu, Zongzhi, University of Colorado, United States of America
local.contributor.affiliationLozupone, Catherine, University of Colorado, United States of America
local.contributor.affiliationMcDonald, Daniel, University of Colorado, United States of America
local.contributor.affiliationRobeson, Michael, University of Colorado, United States of America
local.contributor.affiliationSammut, Raymond, College of Medicine, Biology and Environment, CMBE John Curtin School of Medical Research, Genome Sciences, The Australian National University
local.contributor.affiliationSmit, Sandra, University of Colorado, United States of America
local.contributor.affiliationWakefield, Matthew, College of Medicine, Biology and Environment, CMBE John Curtin School of Medical Research, JCSMR General, The Australian National University
local.contributor.affiliationWidmann, Jeremy, University of Colorado, United States of America
local.contributor.affiliationWikman, Shandy, University of Colorado, United States of America
local.contributor.affiliationWilson, Stephanie, University of Colorado, United States of America
local.contributor.affiliationYing, Hua, College of Medicine, Biology and Environment, CMBE John Curtin School of Medical Research, Genome Sciences, The Australian National University
local.contributor.affiliationHuttley, Gavin Austin, College of Medicine, Biology and Environment, CMBE John Curtin School of Medical Research, Genome Sciences, The Australian National University
local.identifier.essn1474-760X
local.bibliographicCitation.issue8
local.bibliographicCitation.startpageR171
local.identifier.doi10.1186/gb-2007-8-8-r171
dc.date.updated2016-02-24T09:50:49Z
local.identifier.scopusID2-s2.0-34748893838
CollectionsANU Research Publications

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