HMM Algorithm for Multiple Sequence Alignment using SAM method

[rehaman]

hi can anyone give suggestions hw to use hmm based algorithm for multiple sequence alignment using SAM method

[mfursov]

Hi,
both SAM and HMMER algorithms could be used to compute sequence-to-sequence score.

AFAIK neither SAM nor HMMER are not tools for multiple alignment construction, so they do not provide any theory of how to do it. So this an open subject to research without definite solution.

A long time ago HMMER1 package had a tool named 'hmmt'. Here what Eddy wrote in his guide about it:

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Can I build a model from unaligned sequences? In principle, profile HMMs can be trained
from unaligned sequences; however, this functionality is temporarily withdrawn from HMMER. I recommend CLUSTALW as an excellent, freely available multiple sequence alignment program.
The original hmmt profile HMM training program from HMMER 1 is also still available, from
ftp://ftp.genetics.wustl.edu/pub/edd...er-1.8.4.tar.Z
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And here the link to the manual to this tool: [Only registered users see links. ]

After you have HMM profile built you can align any number of sequences to it one by one and get multiple alignment.