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[Computational-biology] Point Specific Mutation Matrix vs. profile HMM ?

harald please_noSpam at gmx.de
Sun Feb 12 09:40:08 EST 2006

Hi there.

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,

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