Search results
Results from the WOW.Com Content Network
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 ]
The CDD from NCBI amalgamates data from several different sources; Protein FAMilies (PFAM), Simple Modular Architecture Research Tool (SMART), Cluster of Orthologous Genes (COGs), and NCBI's own curated sequences. The data in SMID is derived from the Protein Data Bank (PDB), a database of known protein crystal structures.
CDD content includes NCBI manually curated domain models and domain models imported from a number of external source databases (Pfam, SMART, COG, PRK, TIGRFAMs).What is unique about NCBI-curated domains is that they use 3D-structure information to explicitly define domain boundaries, align blocks, amend alignment details, and provide insights into sequence/structure/function relationships.
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:
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 ...
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
Pfam, [21] a protein family database; Rfam, [22] an RNA family database; TreeFam, [23] a database of phylogenetic trees for animal genes; WormBase, [24] a database on the biology and sequence of the model organism C. elegans and other related Nematodes. WormBase ParaSite, a database for the genomics for parasitic helminths (both Nematodes and ...
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.