[ssml] Hmmalign

[Mensur Dlakic]

If your intention is to do this using hmmalign (as the subject of your 
message implies), take your query sequence and a member of the seed 
alignment used to make the HMM and put them into fasta_file. Then do:

hmmalign -o output_file HMM fasta_file

Of course, you can take as many sequences from the seed alignment as you 
want. This doesn't mean that the alignment will be optimal - it will only 
be optimal according to the HMM used.

Hope this helps,

Mensur


At 02:21 PM 5/19/2005, you wrote:
>Dear All,
>
>Is there a way I can get individual alignments for a query sequence with the
>members of the HMM profile?
>
>Thanks in advance.
>
>Best
>
>Rajesh

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| Mensur Dlakic, PhD                | Tel: (406) 994-6576                |
| Department of Microbiology        | Fax: (406) 994-4926                |
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