title: PyCogent: a toolkit for making sense from sequence.
abstract: 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 hardware and operating systems, and is available under the general public license from http://sourceforge.net/projects/pycogent.
authors: Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA. rob@spot.colorado.edu
authors: Rob
authors: R
authors: Knight
authors: Peter
authors: P
authors: Maxwell
authors: Amanda
authors: A
authors: Birmingham
authors: Jason
authors: J
authors: Carnes
authors: J Gregory
authors: JG
authors: Caporaso
authors: Brett C
authors: BC
authors: Easton
authors: Michael
authors: M
authors: Eaton
authors: Micah
authors: M
authors: Hamady
authors: Helen
authors: H
authors: Lindsay
authors: Zongzhi
authors: Z
authors: Liu
authors: Catherine
authors: C
authors: Lozupone
authors: Daniel
authors: D
authors: McDonald
authors: Michael
authors: M
authors: Robeson
authors: Raymond
authors: R
authors: Sammut
authors: Sandra
authors: S
authors: Smit
authors: Matthew J
authors: MJ
authors: Wakefield
authors: Jeremy
authors: J
authors: Widmann
authors: Shandy
authors: S
authors: Wikman
authors: Stephanie
authors: S
authors: Wilson
authors: Hua
authors: H
authors: Ying
authors: Gavin A
authors: GA
authors: Huttley
mesh_terms: D000818:Animals; D019313:BRCA1 Protein / Q000235:genetics; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D006801:Humans; D010802:Phylogeny; D011487:Protein Conformation; D020560:Proteobacteria / Q000145:classification / Q000235:genetics; D017421:Sequence Analysis / Q000379:methods*; D012984:Software; D014841:von Willebrand Factor / Q000737:chemistry / Q000235:genetics
chemical_list: D019313:BRCA1 Protein; D014841:von Willebrand Factor
references: Genome Res. 2002 Apr;12(4):656-64
references: 11932250
references: J Mol Biol. 1990 Oct 5;215(3):403-10
references: 2231712
references: Science. 2003 Dec 12;302(5652):1960-3
references: 14671302
references: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D101-3
references: 14681368
references: Nucleic Acids Res. 2004;32(5):1792-7
references: 15034147
references: BMC Bioinformatics. 2004 Jan 5;5:1
references: 14706121
references: J Comput Biol. 2004;11(2-3):413-28
references: 15285899
references: Biochim Biophys Acta. 2004 Aug 12;1679(2):95-106
references: 15297143
references: Mol Biol Evol. 2004 Sep;21(9):1760-8
references: 15190129
references: Genome Biol. 2004;5(10):R80
references: 15461798
references: Bioinformatics. 1999 Mar;15(3):211-8
references: 10222408
references: Mol Biol Evol. 2005 Apr;22(4):1107-18
references: 15689528
references: Mol Biol Evol. 1987 Jul;4(4):406-25
references: 3447015
references: Bioinformatics. 2006 Nov 1;22(21):2688-90
references: 16928733
references: Comput Appl Biosci. 1992 Jun;8(3):275-82
references: 1633570
references: Mol Biol Evol. 1994 Sep;11(5):715-24
references: 7968485
references: Mol Biol Evol. 1994 Sep;11(5):725-36
references: 7968486
references: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references: 7984417
references: Genetics. 1995 Feb;139(2):993-1005
references: 7713447
references: Proc Int Conf Intell Syst Mol Biol. 1994;2:28-36
references: 7584402
references: Mol Biol Evol. 1996 Jan;13(1):93-104
references: 8583911
references: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references: 9254694
references: Comput Appl Biosci. 1997 Oct;13(5):555-6
references: 9367129
references: Genetics. 1998 Mar;148(3):929-36
references: 9539414
references: J Biol Chem. 1998 Apr 24;273(17):10396-401
references: 9553097
references: Bioinformatics. 2000 Apr;16(4):383-94
references: 10869037
references: Nat Genet. 2000 Aug;25(4):410-3
references: 10932184
references: Hum Mol Genet. 2001 Mar 15;10(6):591-7
references: 11230178
references: Hum Mol Genet. 2001 Oct 1;10(21):2319-28
references: 11689479
references: Hum Mutat. 2002 Feb;19(2):149-64
references: 11793474
references: BMC Bioinformatics. 2005;6:130
references: 15921531
references: Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10557-62
references: 16000407
references: Hum Mutat. 2005 Nov;26(5):446-54
references: 16173033
references: Appl Environ Microbiol. 2005 Dec;71(12):8228-35
references: 16332807
references: BMC Bioinformatics. 2006;7:1
references: 16393334
references: Mol Cell Proteomics. 2006 Aug;5(8):1520-32
references: 16769708
references: BMC Bioinformatics. 2006;7:371
references: 16893466
references: Nucleic Acids Res. 2003 Jul 1;31(13):3450-60
references: 12824344