[Bioperl-l] clustalw to maf format

Bernd Web bernd.web at gmail.com
Mon Aug 2 17:25:52 EDT 2010


Hi Shalabh,

This ConvertAlign does not write maf either, it only reads it (i made
it). I found some other converters on the web but they do not export
to maf format either...

http://biotechvana.uv.es/servers/afc/main.php
http://www.hiv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html

Galaxy has a MAF to Fasta converter:
http://main.g2.bx.psu.edu/root?tool_id=MAF_To_Fasta1


Regards,
Bernd


On Mon, Aug 2, 2010 at 10:53 PM, shalabh sharma
<shalabh.sharma7 at gmail.com> wrote:
> Hi Russell,
>            Thanks for the reply, but i  have around 400 alignments and some
> huge ones :(
>
> Thanks
> Shalabh
>
>
> On Mon, Aug 2, 2010 at 4:25 PM, Smithies, Russell <
> Russell.Smithies at agresearch.co.nz> wrote:
>
>> This might work if you only have a few:
>> http://www.ibi.vu.nl/programs/convertalignwww/
>>
>> --Russell
>>
>>
>> > -----Original Message-----
>> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> > bounces at lists.open-bio.org] On Behalf Of shalabh sharma
>> > Sent: Tuesday, 3 August 2010 7:45 a.m.
>> > To: bioperl-l
>> > Subject: [Bioperl-l] clustalw to maf format
>> >
>> > Hi,
>> >     I am trying to convert clustalw to maf format.
>> > I am trying to use AlignIO for that but its not working.
>> >
>> > Its giving me the following error:
>> >
>> > EXCEPTION Bio::Root::NotImplemented -------------
>> > MSG: Abstract method "Bio::AlignIO::maf::write_aln" is not implemented by
>> > package Bio::AlignIO::maf.
>> > This is not your fault - author of Bio::AlignIO::maf should be blamed!
>> >
>> > STACK Bio::Root::RootI::throw_not_implemented
>> > /Library/Perl/5.8.8/Bio/Root/RootI.pm:707
>> > STACK Bio::AlignIO::maf::write_aln /Library/Perl/5.8.8/Bio/AlignIO/
>> > maf.pm:176
>> > STACK Bio::AlignIO::PRINT /Library/Perl/5.8.8/Bio/AlignIO.pm:492
>> > STACK toplevel msf2mafy.pl:11
>> >
>> >
>> > Is there any other way i can convert clustalw to maf?
>> >
>> > I would really appreciate if anyone can help me out.
>> >
>> > Thanks
>> > Shalabh
>> > _______________________________________________
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>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
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