[Bioperl-l] Generating a consensus sequence from a Clustal alignment

Thomas Sharpton thomas.sharpton at gmail.com
Mon Oct 18 22:30:40 EDT 2010


While the tools you mention are sufficient, you might be interested to  
know that HMMER can also generate consensus sequences. Briefly, you  
would use the alignment you generated with clustal (or any other  
multiple sequence alignment tool) to build an HMM via the hmmbuild  
function. You can then emit a consensus sequence from the HMM file  
using the hmmemit function:

hmmemit -c HMM_file.hmm

Just FYI.

T

On Oct 18, 2010, at 5:02 PM, Bill Stephens wrote:

> So, I've got the SimpleAlign running. It looks like it's running the
> alignment based upon the input sequence location only (first residue  
> from
> each sequence).  This is not what I need.
>
> I'm back to to clustal, tcoffee or dalign.
>
> Bill
>
> On Mon, Oct 18, 2010 at 12:09 PM, Jun Yin <jun.yin at ucd.ie> wrote:
>
>> Hi, Bill,
>>
>> You may consider to use consensus_iupac or consensus_string methods  
>> in
>> Bio::SimpleAlign to generate consensus sequence.
>>
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>>
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris  
>> Fields
>> Sent: Monday, October 18, 2010 3:55 PM
>> To: Bill Stephens
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] Generating a consensus sequence from a  
>> Clustal
>> alignment
>>
>> Bill,
>>
>> Actually, the page you reached at Pasteur is not Pise, but Mobyle  
>> (their
>> replacement for the older Pise tools).  The Pise modules were in
>> BioPerl-Run, but they were deprecated a few years ago and removed  
>> from the
>> latest BioPerl-Run releases b/c the remote service is no longer  
>> active;
>> there is no Perl-based replacement for Mobyle interaction.
>>
>> Have you thought about just using the functionality within the
>> Bio::SimpleAlign class to generate the consensus?  I'm pretty sure  
>> there
>> are
>> methods in place to do that.
>>
>> chris
>>
>> On Oct 18, 2010, at 8:58 AM, Bill Stephens wrote:
>>
>>> All,
>>>
>>> I'm in my first week with bioperl for a class project (although  
>>> I've used
>>> Perl for years). I've successfully run a clustal alignment of  
>>> several DNA
>>> sequences to produce the aln and dnd files. Now I would like to  
>>> generate
>> a
>>> consensus sequence from the alignment.  I see that Pise Cons does  
>>> this
>>> satisfactorily on my example data (
>>> http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) .  
>>> However,
>> I'm
>>> not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1
>> distribution
>>> that I installed.
>>>
>>> Is this another module that I need to install separately?
>>>
>>> "cpan[2]> m /Pise/
>>> Module    Bio::Tools::Run::AnalysisFactory::Pise
>>> (BIRNEY/bioperl-run-1.4.tar.gz)
>>> Module    Bio::Tools::Run::PiseApplication
>> (BIRNEY/bioperl-run-1.4.tar.gz)"
>>>
>>> Bill S.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
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