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 jen@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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The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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