[Biopython] Biopython Digest, Vol 105, Issue 14

[Nasos Dousis]

Frank,

Thanks for your reply and suggestion.  I tried that command line with
ClustalW2 and a number of variations:

clustalw2 -sequences -profile1=mas_file.aln
-profile2=new_sequences.fas (.aln = clustal format)
clustalw2 -sequences -profile1=mas_file.aln -profile2=new_sequences.aln
clustalw2 -sequences -profile1=new_sequences.fas -profile2=mas_file.aln
clustalw2 -sequences -profile2=new_sequences.fas -profile1=mas_file.aln
clustalw2 -profile1=mas_file.aln -profile2=new_sequences.fas
clustalw2 -profile1=mas_file.aln -profile2=mas_file.aln
clustalw2 -profile1=mas_file.aln

etc

and I always get the following error:

==================================================================
[ndousis at linux-machine ~]$ clustalw2 -profile1=mas_file.aln
-profile2=new_sequences.aln



 CLUSTAL 2.1 Multiple Sequence Alignments


Sequence format is CLUSTAL
ERROR: There are no sequences in profile2 file.
==================================================================

Nevertheless, I implemented a simple version of Needleman-Wunsch to
align my sequence to the MSA and choose the highest scoring alignment.

Thanks and kind regards,
Nasos


On Mon, Sep 26, 2011 at 9:00 AM,  <biopython-request at lists.open-bio.org> wrote:
> Message: 3
> Date: Mon, 26 Sep 2011 16:54:15 +0200
> From: Frank Kauff <fkauff at biologie.uni-kl.de>
> Subject: Re: [Biopython] align single sequence to MSA
> To: biopython at lists.open-bio.org
> Message-ID: <4E809217.5040004 at biologie.uni-kl.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi,
>
> Yes, clustal can do this easily. If I remember correctly the command
> line should be something like
>
> clustalw -sequences -profile1=mas_file.fas -profile2=new_sequences.fas
>
> Frank
>
>
> On 09/12/2011 03:00 AM, Nasos Dousis wrote:
>> Hello,
>>
>> First, thank you to everyone who has contributed to the BioPython
>> codebase and to the mailing list.
>>
>> I have a FASTA sequence, and I'd like to find the optimal alignment of
>> that sequence to an MSA.  I don't want to alter the MSA-- I just want
>> to map the single sequence onto the MSA.  Is there a simple way to do
>> this by ClustalW or MUSCLE?
>>
>> Thanks,
>> Nasos
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>
>
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> End of Biopython Digest, Vol 105, Issue 14
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