However, the calibration only has to be performed once, as the extreme value distribution parameters are stored with the profile HMM and will be used whenever you perform profile HMM-sequence database searches. Creating temp file for input to hmmcalibrate. The profile HMM itself wasn't changed but several new lines were added to the file. The line labeled EVD contains the parameters mu and lambda that describe the extreme value distribution of the calibration search. The values on this line are used by HmmerSearch and HmmerPfam.
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.