HMMPFAM
HMMPFAM is used to search one or more sequences against the Pfam Hidden Markov Model (HMM) database. HMMPFAM reads a sequence and compares it against a database of all the HMMs, looking for significant sequence similarities between query and HMMs. The program reports:
- a ranked list of the best scoring HMMs
- a list of the best scoring domains in order of their occurrence in the sequence
- alignments for all the best scoring domains.
All sequences scoring above the -E and -T cutoffs are shown in the first list, then every domain found in this list is shown in the second list of domain hits. If desired, E-value and bit score thresholds may also be applied to the domain list using the --domE and --domT options. A sequence score may be higher than a domain score for the same sequence if there is more than one domain in the sequence; the sequence score takes into account all the domains.
Manual: hmmr_man.pdf
INPUT = Protein Sequence.
TEST INPUT FILES
Input file: hmmpfam_in.txt
TEST OUTPUT FILES
Output file: hmmpfam_out1.txt