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

Erik L. L. Sonnhammer | Zendy

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

Author(s) -

Erik L. L. Sonnhammer

Publication year - 1998

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/26.1.320

Subject(s) - biology , hidden markov model , computational biology , ensembl , genome , protein family , sequence alignment , multiple sequence alignment , protein domain , genetics , sanger sequencing , sequence (biology) , sequence analysis , hypothetical protein , similarity (geometry) , bioinformatics , peptide sequence , genomics , dna sequencing , gene , computer science , artificial intelligence , image (mathematics)

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.

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