Erika,

Although Galaxy doesn't have a suitable mapping tool for fasta format
sequences, you can use the Galaxy clustalw tool option to output a
fasta format file and then upload that fasta file to the ncbi Blast
tool at http://blast.ncbi.nlm.nih.gov/Blast.cgi to find where the
sequences align - blast allows mapping of sequences on multiple
organisms.

I hope this helps in your research

On Fri, Apr 13, 2012 at 10:36 AM, Jennifer Jackson <j...@bx.psu.edu> wrote:
> Hi Erika,
>
> Unfortunately, Galaxy does not have a parser tool to transform clustal
> datatypes into tab-coordinate based files.
>
> Sorry we couldn't help!
>
> Best,
>
> Jen
> Galaxy team
>
> On 4/12/12 8:07 AM, Erika Kruse wrote:
>>
>> Hello,
>>
>> I imported a sequence alignment file from clustalw. How can I generate a
>> list of the coordinates of the matching regions?
>>
>> Thank you.
>>
>> Erika
>>
>>
>>
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> ___________________________________________________________
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-- 
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

___________________________________________________________
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