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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 ]
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.
This list of protein subcellular localisation prediction tools includes software, databases, and web services that are used for protein subcellular localization prediction. Some tools are included that are commonly used to infer location through predicted structural properties, such as signal peptide or transmembrane helices , and these tools ...
InterPro is a database of protein families, protein domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences [2] in order to functionally characterise them.
The output of HHpred and HHsearch is a ranked list of database matches (including E-values and probabilities for a true relationship) and the pairwise query-database sequence alignments. HHblits, a part of the HH-suite since 2001, builds high-quality multiple sequence alignments (MSAs) starting from a single query sequence or a MSA.
protein families database of alignments and HMMs Protein sequence databases Human Proteinpedia: Institute of Bioinformatics (IOB), Bangalore and Johns Hopkins University, The human Proteinpedia is based on HPRD (Human protein reference database)which is a repository hosting over 30,000 human proteins.
TIGRFAMs is a database of protein families designed to support manual and automated genome annotation. [1] [2] [3] Each entry includes a multiple sequence alignment and hidden Markov model (HMM) built from the alignment. Sequences that score above the defined cutoffs of a given TIGRFAMs HMM are assigned to that protein family and may be ...
A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220.