Hmmer is a suite of programs which use profile hidden Markov models (profile HMMs) to model the primary structure consensus of a family of protein or nucleic acid sequences.
HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
You submit sequence in the following format:
>2abl_A mol:protein length:163 ABL
For more information see: Finn RD, Clements J, Eddy DR. HMMER web server: interactive sequence milarity searching. Nucleic Acids Research. Web Server Issue 2011;39:W29-W37. Search parameters guide at http://hmmer.janelia.org/help/search