protein domain prediction

MkDom2 is the program used routinely to build each new release of ProDom. The algorithm relies on the assumption that the shortest amino acid sequence corresponds to a single domain, and may be used as a query to screen the database with the psi-blast program, in order to cluster homologous domains. To build ProDom, we run this program on the UniProt (swissprot/trembl) Knowledge Database, but it can be run on any set of protein sequences in a fasta file.

Inputs:

• a file containing the sequences to analyse in fasta format

SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. More than 700 domain families found in signaling, extracellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. The webservice accepts either a protein sequence or Uniprot/Ensembl protein identifiers. If both a sequence and an ID are supplied, ID will be used.