[Bio-Linux] hmmer tutorial help

[Graham Thomas]

Hi All,

I am just getting started with biolinux.

I am trying to follow the 'HMMER users guide (Eddy 2003)' tutorial (pg 20).
First command is;

> hmmbuild globin.hmm globins50.msf

But I get this msg;

> Alignment input open failed.
        couldn't determine alignment input format
        while reading file globins50.msf

The only online reference to this problem I could find was from
laurelslabnotebook.blogspot.co.uk ;

"At first I was aligning the sequences with ClustalOmega
<http://www.ebi.ac.uk/Tools/services/web_clustalo/toolform.ebi> and trying
to put the sequences in .msf
<http://toolkit.tuebingen.mpg.de/reformat/help_params#msf>format, as many
HMMER tutorials show. However, I could not for the life of me figure out
what was wrong and kept getting the following error:
 hmmbuild vno.hmm vno_trainerSeqs.msf
 Alignment input open failed.
    couldn't determine alignment input format
    while reading file vno_trainerSeqs.msf
So I gave up on .msf"

Can anyone advise on what causes this problem and how to fix it?

Many thanks
Graham
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