title: Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily.
abstract: BACKGROUND
  Kinases of the eukaryotic protein kinase superfamily are key regulators of most aspects eukaryotic cellular behavior and have provided several drug targets including kinases dysregulated in cancers. The rapid increase in the number of genomic sequences has created an acute need to identify and classify members of this important class of enzymes efficiently and accurately.
  
  
  RESULTS
  Kinannote produces a draft kinome and comparative analyses for a predicted proteome using a single line command, and it is currently the only tool that automatically classifies protein kinases using the controlled vocabulary of Hanks and Hunter [Hanks and Hunter (1995)]. A hidden Markov model in combination with a position-specific scoring matrix is used by Kinannote to identify kinases, which are subsequently classified using a BLAST comparison with a local version of KinBase, the curated protein kinase dataset from www.kinase.com. Kinannote was tested on the predicted proteomes from four divergent species. The average sensitivity and precision for kinome retrieval from the test species are 94.4 and 96.8%. The ability of Kinannote to classify identified kinases was also evaluated, and the average sensitivity and precision for full classification of conserved kinases are 71.5 and 82.5%, respectively. Kinannote has had a significant impact on eukaryotic genome annotation, providing protein kinase annotations for 36 genomes made public by the Broad Institute in the period spanning 2009 to the present.
  
  
  BACKGROUND
  Kinannote is freely available at http://sourceforge.net/projects/kinannote.
authors.affiliation: Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA and Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Goldberg
authors.forename: Allison D
authors.initials: AD
authors.lastname: Griggs
authors.forename: Janet L
authors.initials: JL
authors.lastname: Smith
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Haas
authors.forename: Jennifer R
authors.initials: JR
authors.lastname: Wortman
authors.forename: Qiandong
authors.initials: Q
authors.lastname: Zeng
mesh_terms: D000465:Algorithms; D005057:Eukaryotic Cells / Q000201:enzymology*; D016678:Genome; D020407:Internet; D056510:Position-Specific Scoring Matrices; D011494:Protein Kinases / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D020543:Proteome / Q000235:genetics; D012985:Software Design
chemical_list: D020543:Proteome; D011494:Protein Kinases
references.citation: Microbes Infect. 2012 Aug;14(10):796-810
references.pmid: 22587893
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D153-5
references.pmid: 14681382
references.citation: Genome Res. 2012 Dec;22(12):2478-88
references.pmid: 22813931
references.citation: mBio. 2012 Sep 04;3(5):e00259-12
references.pmid: 22951933
references.citation: Genome Res. 2003 Sep;13(9):2178-89
references.pmid: 12952885
references.citation: Proc Natl Acad Sci U S A. 2010 Jun 29;107(26):11889-94
references.pmid: 20547848
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Science. 2011 May 20;332(6032):930-6
references.pmid: 21511999
references.citation: FASEB J. 1995 May;9(8):576-96
references.pmid: 7768349
references.citation: Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10915-9
references.pmid: 1438297
references.citation: Genome Res. 1998 Oct;8(10):1038-47
references.pmid: 9799791
references.citation: Science. 2002 Dec 6;298(5600):1912-34
references.pmid: 12471243
references.citation: J Am Coll Radiol. 2006 Jun;3(6):413-22
references.pmid: 17412096
references.citation: Proteins. 2008 May 1;71(2):995-1006
references.pmid: 18004777
references.citation: PLoS Genet. 2006 Mar;2(3):e38
references.pmid: 16596165
references.citation: Q Rev Biophys. 2009 Feb;42(1):1-40
references.pmid: 19296866
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D261-70
references.pmid: 22135298
references.citation: PLoS One. 2011;6(12):e28782
references.pmid: 22194913
references.citation: Funct Integr Genomics. 2004 Jul;4(3):163-87
references.pmid: 14740254
references.citation: Protist. 2013 Jan;164(1):2-12
references.pmid: 23083534
references.citation: J Mol Biol. 2005 Sep 2;351(5):956-72
references.pmid: 16051269
references.citation: Trends Microbiol. 2009 Nov;17(11):488-97
references.pmid: 19782570
references.citation: Bioinformatics. 1998;14(9):755-63
references.pmid: 9918945
references.citation: Nat Genet. 2013 May;45(5):495-500
references.pmid: 23525074
references.citation: Nature. 2010 Aug 5;466(7307):720-6
references.pmid: 20686567
references.citation: Protoplasma. 2012 Jan;249(1):3-19
references.pmid: 21424613
references.citation: Science. 2003 Jun 13;300(5626):1703-6
references.pmid: 12805537
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D244-50
references.pmid: 18974176
references.citation: BMC Evol Biol. 2011 Nov 02;11:321
references.pmid: 22047078
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301
references.pmid: 22127870
references.citation: Genome Biol. 2011 Jul 25;12(7):R66
references.pmid: 21787419
references.citation: Trends Biochem Sci. 1997 Nov;22(11):444-6
references.pmid: 9397688
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D348-52
references.pmid: 23197659
references.citation: Trends Biochem Sci. 2002 Oct;27(10):514-20
references.pmid: 12368087
references.citation: Cell Host Microbe. 2010 Aug 19;8(2):208-18
references.pmid: 20709297
references.citation: Eukaryot Cell. 2008 Aug;7(8):1238-45
references.pmid: 18539886
references.citation: Proc Natl Acad Sci U S A. 2011 May 31;108(22):9166-71
references.pmid: 21536894
references.citation: Nat Genet. 2012 Sep;44(9):1046-50
references.pmid: 22863733
references.citation: PLoS Comput Biol. 2005 Oct;1(5):e49
references.pmid: 16244704
references.citation: PLoS Biol. 2006 Sep;4(9):e286
references.pmid: 16933976
references.citation: BMC Genomics. 2011 Sep 30;12:478
references.pmid: 21962082
references.citation: Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9674-9
references.pmid: 18621719