prodom

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

fetchProDom is a set of five different webservices that interrogates the ProDom database.

• fetchdom: Enter one or several (separated by spaces) ProDom AC (eg PD000039) and it returns the family(ies) description in prodom format.
• fetchdom_fasta: same as above with the results given in fasta format.