I am a computer engineering student. I am entitled for a project in HMMER on MIC Card. I wanted to know how is a profile made out of the .sto or .msf file using hmmbuild function in HMMER? I wanted to know the meaning of all the numbers calculated of matches, insertions and deletions and the way they are arranged at the output.
These should help you get an idea of what HMMER is supposed to do and how it is supposed to achieve that. Feel free to ask more specific questions as you read up!