The HH-suite comes with a number of useful databases of profile HMMs that can be searched using HHblits and HHsearch, among them a clustered version of the UniProt database, HMMs for the protein data bank of protein structures, for the Pfam database of protein family alignments, the SCOP database of structural protein domains, and many more.
The HHpred server and the HH-suite software package offer many popular, regularly updated databases, such as the Protein Data Bank, as well as the InterPro, Pfam, COG, and SCOP databases.
HMMER is the core utility that protein family databases such as Pfam and InterPro are based upon.
Stockholm format is a Multiple sequence alignment format used by Pfam and Rfam to disseminate protein and RNA sequence alignments
Pfam |