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bioinformatics toolbox- command from turoial won't work

Fri, 13 Nov 2009 14:26:09 -0700

I am trying to do an HMM alignment, and I am talking the commands straight out of the tutorial, and I am getting errors. It is funny, because I can do other tutorials, its not like the whole thing is broken.
This is what happens:

hmmmodel = gethmmprof('PF00002')

is the command.

error:
??? Error using ==> pfamhmmread at 70
Input is not a valid PFAM file.

Error in ==> getsangerdata at 180
out = pfamhmmread(s);

Error in ==> gethmmprof at 82
model = getsangerdata(accessnum,'database','hmm',varargin{ :});

Does anyone know what is going on?
Thanks.
Mark

Re: bioinformatics toolbox- command from turoial won't work

Mon, 07 Dec 2009 16:45:08 -0700

Hi Mark:

Try this instead:

<for example Pfam Id= PF01596>

seed_seqs = gethmmalignment(1596,'type','seed');
seqdisp(seed_seqs(),'row',80)

-Mia

Re: bioinformatics toolbox- command from turoial won't work

Mon, 07 Dec 2009 16:46:54 -0700

Hi Mark:

<for example Pfam Id= PF01596>
Try this instead:

seed_seqs = gethmmalignment(1596,'type','seed');
seqdisp(seed_seqs(),'row',80)

-Mia