Question: Clustal alignments for ref_seq genes across specific mammals
gravatar for graham.m.richardson
4.3 years ago by
United States
graham.m.richardson10 wrote:


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?



ADD COMMENTlink modified 4.3 years ago by Jennifer Hillman Jackson25k • written 4.3 years ago by graham.m.richardson10
gravatar for Jennifer Hillman Jackson
4.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi Graham,

There are several options in the Toolshed. Search by "clust" and "assem" to see the list.

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.

Another choice is DNAClust for local/cloud use:

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.

Hope this helps you to find the best path! Jen, Galaxy team

ADD COMMENTlink written 4.3 years ago by Jennifer Hillman Jackson25k
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