[Bio-Linux] hmmer tutorial help

[Tim Booth]

Hi Graham,

This tutorial is out of date and refers to hmmer2.  hmmer2 is still
available on Bio-Linux for backwards compatibility but you have to call
it explicitly - this works:

$ hmm2build globin.hmm globins50.msf

And similarly add a 2 to other command names.

But I'd recommend that you are best off working with HMMER3.  It's much
improved over version 2 and there is a newer tutorial:

ftp://selab.janelia.org/pub/software/hmmer/CURRENT/Userguide.pdf

We really do need to update the documentation for tools on Bio-Linux,
I've just been too short of time to work through it all.

Cheers,

TIM

On Mon, 2015-05-04 at 10:50 +0100, Graham Thomas wrote:
> 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 and trying to
> put the sequences in .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

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

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