Using Pfam

Pfam can be used with the genewisedb or the estwisedb program with the -pfam flag. Usually you want to also use the -dnas (single DNA sequence flag) as well. An example run would be

genewisedb -pfam Pfam -dnas myseq.fa

If you have set up the HMMER package to work with Pfam using the enviroment variable HMMERDB, Wise2 will also pick that up as well.