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Literature DB >> 9399864

Pfam: multiple sequence alignments and HMM-profiles of protein domains.

E L Sonnhammer¹, S R Eddy, E Birney, A Bateman, R Durbin.

Abstract

Pfam contains multiple alignments and hidden Markov model based profiles (HMM-profiles) of complete protein domains. The definition of domain boundaries, family members and alignment is done semi-automatically based on expert knowledge, sequence similarity, other protein family databases and the ability of HMM-profiles to correctly identify and align the members. Release 2.0 of Pfam contains 527 manually verified families which are available for browsing and on-line searching via the World Wide Web in the UK at http://www.sanger.ac.uk/Pfam/ and in the US at http://genome.wustl. edu/Pfam/ Pfam 2.0 matches one or more domains in 50% of Swissprot-34 sequences, and 25% of a large sample of predicted proteins from the Caenorhabditis elegans genome.

Entities: Species

Mesh：

Substances：
Proteins

Year: 1998 PMID： 9399864 PMCID： PMC147209 DOI： 10.1093/nar/26.1.320

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

10 in total

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Authors: S Henikoff; S Pietrokovski; J G Henikoff
Journal: Nucleic Acids Res Date: 1998-01-01 Impact factor: 16.971

2. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998.

Authors: A Bairoch; R Apweiler
Journal: Nucleic Acids Res Date: 1998-01-01 Impact factor: 16.971

Review 3. Hidden Markov models.

Authors: S R Eddy
Journal: Curr Opin Struct Biol Date: 1996-06 Impact factor: 6.809

4. Pfam: a comprehensive database of protein domain families based on seed alignments.

Authors: E L Sonnhammer; S R Eddy; R Durbin
Journal: Proteins Date: 1997-07

5. Connecting protein family resources using the proWeb network.

Authors: S Henikoff; S A Endow; E A Greene
Journal: Trends Biochem Sci Date: 1996-11 Impact factor: 13.807

6. The PROSITE database, its status in 1997.

Authors: A Bairoch; P Bucher; K Hofmann
Journal: Nucleic Acids Res Date: 1997-01-01 Impact factor: 16.971

7. Novel developments with the PRINTS protein fingerprint database.

Authors: T K Attwood; M E Beck; A J Bleasby; K Degtyarenko; A D Michie; D J Parry-Smith
Journal: Nucleic Acids Res Date: 1997-01-01 Impact factor: 16.971

8. A workbench for large-scale sequence homology analysis.

Authors: E L Sonnhammer; R Durbin
Journal: Comput Appl Biosci Date: 1994-06

9. Hidden Markov models in computational biology. Applications to protein modeling.

Authors: A Krogh; M Brown; I S Mian; K Sjölander; D Haussler
Journal: J Mol Biol Date: 1994-02-04 Impact factor: 5.469

10. Modular arrangement of proteins as inferred from analysis of homology.

Authors: E L Sonnhammer; D Kahn
Journal: Protein Sci Date: 1994-03 Impact factor: 6.725

10 in total

245 in total

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Journal: J Virol Date: 2001-01 Impact factor: 5.103

2. Comparative genome analysis of the pathogenic spirochetes Borrelia burgdorferi and Treponema pallidum.

Authors: G Subramanian; E V Koonin; L Aravind
Journal: Infect Immun Date: 2000-03 Impact factor: 3.441

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Authors: R J Bongaerts; H P Heinz; U Hadding; G Zysk
Journal: Infect Immun Date: 2000-12 Impact factor: 3.441

4. Novel genes coding for lithotrophic sulfur oxidation of Paracoccus pantotrophus GB17.

Authors: C G Friedrich; A Quentmeier; F Bardischewsky; D Rother; R Kraft; S Kostka; H Prinz
Journal: J Bacteriol Date: 2000-09 Impact factor: 3.490

5. The conserved characteristics of DNA-binding domains belonging to the homeodomain class that are associated with coadaptive substitutions of amino acid residues.

Authors: D A Afonnikov; N A Koichanov
Journal: Dokl Biochem Biophys Date: 2001 Sep-Oct Impact factor: 0.788

6. Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases.

Authors: S H Shiu; A B Bleecker
Journal: Proc Natl Acad Sci U S A Date: 2001-08-28 Impact factor: 11.205

7. SUPFAM--a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes.

Authors: Shashi B Pandit; Dilip Gosar; S Abhiman; S Sujatha; Sayali S Dixit; Natasha S Mhatre; R Sowdhamini; N Srinivasan
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971