Literature DB >> 7497123

Maximum discrimination hidden Markov models of sequence consensus.

S R Eddy1, G Mitchison, R Durbin.   

Abstract

We introduce a maximum discrimination method for building hidden Markov models (HMMs) of protein or nucleic acid primary sequence consensus. The method compensates for biased representation in sequence data sets, superseding the need for sequence weighting methods. Maximum discrimination HMMs are more sensitive for detecting distant sequence homologs than various other HMM methods or BLAST when tested on globin and protein kinase catalytic domain sequences.

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Year:  1995        PMID： 7497123     DOI： 10.1089/cmb.1995.2.9

Source DB:  PubMed          Journal:  J Comput Biol        ISSN： 1066-5277            Impact factor:   1.479


  63 in total

1.  Protein Information Resource: a community resource for expert annotation of protein data.

Authors:  W C Barker; J S Garavelli; Z Hou; H Huang; R S Ledley; P B McGarvey; H W Mewes; B C Orcutt; F Pfeiffer; A Tsugita; C R Vinayaka; C Xiao; L S Yeh; C Wu
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  Sialidase-like Asp-boxes: sequence-similar structures within different protein folds.

Authors:  R R Copley; R B Russell; C P Ponting
Journal:  Protein Sci       Date:  2001-02       Impact factor: 6.725

Review 3.  Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.

Authors:  A A Schäffer; L Aravind; T L Madden; S Shavirin; J L Spouge; Y I Wolf; E V Koonin; S F Altschul
Journal:  Nucleic Acids Res       Date:  2001-07-15       Impact factor: 16.971

4.  The Protein Information Resource: an integrated public resource of functional annotation of proteins.

Authors:  Cathy H Wu; Hongzhan Huang; Leslie Arminski; Jorge Castro-Alvear; Yongxing Chen; Zhang-Zhi Hu; Robert S Ledley; Kali C Lewis; Hans-Werner Mewes; Bruce C Orcutt; Baris E Suzek; Akira Tsugita; C R Vinayaka; Lai-Su L Yeh; Jian Zhang; Winona C Barker
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

5.  Genome sequence of a baculovirus pathogenic for Culex nigripalpus.

Authors:  C L Afonso; E R Tulman; Z Lu; C A Balinsky; B A Moser; J J Becnel; D L Rock; G F Kutish
Journal:  J Virol       Date:  2001-11       Impact factor: 5.103

6.  Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases.

Authors:  Lewyn Li; Eugene I Shakhnovich; Leonid A Mirny
Journal:  Proc Natl Acad Sci U S A       Date:  2003-04-04       Impact factor: 11.205

7.  Regulation of DAF-2 receptor signaling by human insulin and ins-1, a member of the unusually large and diverse C. elegans insulin gene family.

Authors:  S B Pierce; M Costa; R Wisotzkey; S Devadhar; S A Homburger; A R Buchman; K C Ferguson; J Heller; D M Platt; A A Pasquinelli; L X Liu; S K Doberstein; G Ruvkun
Journal:  Genes Dev       Date:  2001-03-15       Impact factor: 11.361

8.  PIRSF: family classification system at the Protein Information Resource.

Authors:  Cathy H Wu; Anastasia Nikolskaya; Hongzhan Huang; Lai-Su L Yeh; Darren A Natale; C R Vinayaka; Zhang-Zhi Hu; Raja Mazumder; Sandeep Kumar; Panagiotis Kourtesis; Robert S Ledley; Baris E Suzek; Leslie Arminski; Yongxing Chen; Jian Zhang; Jorge Louie Cardenas; Sehee Chung; Jorge Castro-Alvear; Georgi Dinkov; Winona C Barker
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

9.  The Protein Information Resource.

Authors:  Cathy H Wu; Lai-Su L Yeh; Hongzhan Huang; Leslie Arminski; Jorge Castro-Alvear; Yongxing Chen; Zhangzhi Hu; Panagiotis Kourtesis; Robert S Ledley; Baris E Suzek; C R Vinayaka; Jian Zhang; Winona C Barker
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

10.  BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases.

Authors:  Konstantinos Bimpikis; Aidan Budd; Rune Linding; Toby J Gibson
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971
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