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Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. [ 1 ] [ 2 ] [ 3 ] The latest version of Pfam, 37.0, was released in June 2024 and contains 21,979 families. [ 4 ]
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Stockholm format is a multiple sequence alignment format used by Pfam, Rfam and Dfam, to disseminate protein, RNA and DNA sequence alignments. [1] [2] [3] The alignment editors Ralee, [4] Belvu and Jalview support Stockholm format as do the probabilistic database search tools, Infernal and HMMER, and the phylogenetic analysis tool Xrate.
The databases in the table below are selected from the databases listed in the Nucleic Acids Research (NAR) databases issues and database collection and the databases cross-referenced in the UniProtKB. Most of these databases are cross-referenced with UniProt / UniProtKB so that identifiers can be mapped to each other. [15] Proteins in human:
Download as PDF; Printable version; In other projects ... PANDIT is a database of multiple sequence alignments and phylogenetic trees ... Pfam: database of protein ...
This is template for a protein family/domain as defined in biological databases such as Pfam. Template parameters [Edit template data] Parameter Description Type Status Symbol Symbol no description Line optional Name Name no description Line optional Image image fill in "NONE" if not needed to suppress the tracking category File optional Width width Width for image String optional Caption ...
Several biological databases document protein superfamilies and protein folds, for example: Pfam - Protein families database of alignments and HMMs; PROSITE - Database of protein domains, families and functional sites; PIRSF - SuperFamily Classification System; PASS2 - Protein Alignment as Structural Superfamilies v2
The development of protein domain databases such as Pfam (Protein Families Database) [10] allow us to find known domains within a query sequence, providing evidence for likely functions. The dcGO website [ 11 ] contains annotations to both the individual domains and supra-domains (i.e., combinations of two or more successive domains), thus via ...