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Question: Alignment Coordinates
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gravatar for Erika Kruse
6.6 years ago by
Erika Kruse • 10
Erika Kruse • 10 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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modified 6.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.6 years ago by Erika Kruse • 10
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gravatar for Jennifer Hillman Jackson
6.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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
ADD COMMENT • link written 6.6 years ago by Jennifer Hillman Jackson ♦ 25k
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 -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
ADD REPLY • link written 6.6 years ago by fubar ♦ 1.1k
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