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Question: Clustal alignments for ref_seq genes across specific mammals
1
gravatar for graham.m.richardson
4.3 years ago by
graham.m.richardson • 10
United States
graham.m.richardson • 10 wrote:

Hello

I'm trying to do a gene-by-gene phylogenetic analysis between several mammalian species. The only way I have found to do this, so far, is to import the relevant .maf files for individual gene loci, convert the files to FASTA format (retaining only my species of interest), and then performing ClustalW analysis on the FASTA files for each gene.

My question is, is there a faster way to do this so that I can get this type of data for each of the annotated human genes in a reasonable timeframe?

Thanks!

Graham
alignment galaxy clustering phylogenetic • 865 views
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modified 4.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.3 years ago by graham.m.richardson • 10
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gravatar for Jennifer Hillman Jackson
4.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hi Graham,

There are several options in the Toolshed. Search by "clust" and "assem" to see the list.
http://usegalaxy.org/toolshed
http://toolshed.g2.bx.psu

This includes ClustalW for use on a cloud/local - which with dedicated resources and custom parameter settings, would go quicker. Especially if a workflow was utilized.
http://toolshed.g2.bx.psu.edu/view/devteam/clustalw

Another choice is DNAClust for local/cloud use:
http://toolshed.g2.bx.psu.edu/view/john-mccallum/dnaclust

And some Public Galaxy servers have a phylogenetic focus. Perhaps see if any meet your goals? Search for "phylo", "meta" and "clust" to start with. You'll see that most focus on microbes, or protein sequence, but not all. Worth a look, and this list updates frequently.
http://wiki.galaxyproject.org/PublicGalaxyServers

Hope this helps you to find the best path! Jen, Galaxy team
ADD COMMENT • link written 4.3 years ago by Jennifer Hillman Jackson ♦ 25k
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