I am a student in computer-science working on my first project in
sequence-analysis. My first step to do is to extract a some homologs of
a query-protein from a big database. According to my investigations in
textbooks and the web, I am goint to use PSI-BLAST or HMMER. According
to my impressions, I can not see a big difference between the Point
Specific Mutation Matrix which is used by PSI-BLAST and the profile HMM
used by HMMER, except the possibility to compute a profile from
unaligned sequences in the case of the profile HMM.
Now I have two questions:
1 - Are the following both approaches nearly equivalent?
A - Conduct a BLAST-Search with the query-protein.
Take the first hits and make a multiple alignment by CLUSTALW or alike.
Use this alignment to train a HMM model.
Use the hmmsearch to search the database with the model.
B - Use two iterations of PSI-BLAST to search for the query-protein.
2 - the HMMER-tool hmmt which was used to build a profile HMM out of an
unaligned set of sequences is not part of HMMER anymore. Does anyone
knows why? Is it generally better to multiple align a set of sequences
before training a HMM model instead of using hmmt?
With kind regards,