[DIYbio] Re: protein consensus sequence recognition site prediction software

It helps to better understand the domain structure of TOR1 to focus on regions of interest. You can use Hidden Markov Models to see which parts of TOR1's amino acids map to domains found in other molecules. It is a statistical approach and sounds quite complex but practically it is quite simple to do, much like submitting an amino acid sequence for BLAST analysis. To do this you can search your FASTA TOR1 file against the PFAM database. I love this database since it shows the awesomeness of evolution - one molecule at a time! With all the genome data being pumped into GenBank the PFAM database automatically troll new protein sequences and incorporates those results in their dataset.