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The general purpose of the Pfam database is to provide a complete and accurate classification of protein families and domains. [5] Originally, the rationale behind creating the database was to have a semi-automated method of curating information on known protein families to improve the efficiency of annotating genomes. [6]
Describes protein families and domain architectures in complete genomes. Protein families are formed using a Markov clustering algorithm, followed by multi-linkage clustering according to sequence identity. Mapping of predicted structure and sequence domains is undertaken using hidden Markov models libraries representing CATH and Pfam domains ...
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. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known ...
This type A domain is the prototype for a protein superfamily (InterPro: IPR036465; see also Pfam clan). The vWA domain is found in various plasma proteins: complement factors B, C2, CR3 and CR4; the integrins (I-domains); collagen types VI, VII, XII and XIV; and other extracellular proteins.
A common interface in ProtCID indicates chain-chain or domain-domain interactions that occur in different crystal forms. All protein sequences of known structure in the Protein Data Bank (PDB) [7] are assigned a ”Pfam chain architecture”, which denotes the ordered Pfam [8] assignments for that sequence, e.g. (Pkinase) or (Cyclin_N)_(Cyclin ...
Sequence-based strategies, based on homology search [14] or domain assignment, [15] [16] mostly underestimate TRs due to the presence of highly degenerate repeat units. [17] A recent study to understand and improve Pfam coverage of the human proteome [17] showed that five of the ten largest sequence clusters not annotated with Pfam are repeat ...
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 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 ...
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