I have downloaded the local pfam data base from ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release . There are two databases 1) Pfam-A.fasta.gz 2) Pfam-A.full.gz . The first one consist of sequences in fasta format with PFAM accession id in its header, but it does not contain all the sequences of a family. The second one consist of sequences in stockholm format. I have converted them to fasta, these contain all the sequences related to a family but the sequence header does not contain the PFAM accession id. I've more than 1500 pfam id's, I want to extract all the sequences that fall under a family (or accession id). Every stockholm alignment in (2) is having the pfam id at the top as, for example "#=GF AC PF00406" . How can I get over this..any help will be greatly appreciated.