The database must have been previously indexed with HmmerIndex. Indexes for these have already been created, so they can be used with HmmerFetch without any further processing. Creating temp file for input to hmmfetch . Profile HMM databases supplied with the Wisconsin Package are Pfam and PfamFrag. They each contain profile HMMs for a large number of protein families.
LineUp is a multiple sequence editor used to create multiple sequence alignments.
Pretty displays multiple sequence alignments. ProfileMake makes a profile from a multiple sequence alignment. ProfileSearch uses the profile to search a database for sequences with similarity to the group of aligned sequences. ProfileGap makes optimal alignments between one or more sequences and a group of aligned sequences represented as a profile. ProfileScan finds structural and sequence motifs in protein sequences, using predetermined parameters to determine significance.