<div dir="ltr">Hi All,<br>
<br>
I am just getting started with biolinux.<br>
<br>
I am trying to follow the 'HMMER users guide (Eddy 2003)' tutorial (pg 20).<br>
First command is;<br>
<br>
> hmmbuild globin.hmm globins50.msf<br>
<br>
But I get this msg;<br>
<br>
> Alignment input open failed. <br>
couldn't determine alignment input format<br>
while reading file globins50.msf<br>
<br>
The only online reference to this problem I could find was from <a href="http://laurelslabnotebook.blogspot.co.uk">laurelslabnotebook.blogspot.co.uk</a> ;<br>
<br>
"At first I was aligning the sequences with <a href="http://www.ebi.ac.uk/Tools/services/web_clustalo/toolform.ebi" target="_blank">ClustalOmega</a> and trying to put the sequences in <a href="http://toolkit.tuebingen.mpg.de/reformat/help_params#msf" target="_blank">.msf </a>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:<br>
<div style="font-family:Menlo;font-size:11px">
<span style="color:blue">hmmbuild vno.hmm vno_trainerSeqs.msf</span></div>
<div style="font-family:Menlo;font-size:11px">
<span style="color:magenta">Alignment input open failed.</span></div>
<div style="font-family:Menlo;font-size:11px">
<span style="color:magenta"> couldn't determine alignment input format</span></div>
<div style="font-family:Menlo;font-size:11px">
<span style="color:magenta"> while reading file vno_trainerSeqs.msf</span></div>
So I gave up on .msf"<br>
<br>
Can anyone advise on what causes this problem and how to fix it?<br>
<br>
Many thanks <br>
Graham</div>