Hi John (and Pablo),

Thanks for the ideas. I assume this is similar to the "aaChanges" tool in the standard galaxy setup which I am working with. If I have no luck with that I'll look into the SNPEff tool - is it in the Galaxy toolshed? 

I think that, assuming most of the snps are previously characterised, I can probably get such a list by long winded means. Fingers crossed!

Cheers

David

On 9 Jun 2011, at 19:18, John David Osborne wrote:

Hi David,

I’ve successfully used SNPEff (which can fit into galaxy) to make SNP effect predictions that would effect the proteome, but from genomic not transcriptomic data but I think it might still work on that...

It takes in pileup/vcf format and predicts coding changes, upstream changes, splice acceptor/donor effects, etc...

However I don’t think it will re-create an entire proteome for you, ie) it won’ t output the new set of proteins in FASTA format or anything like that. I don’t know of any tool that does that, but it would be nice!

I cc’d the author of SNPEff in case I am misrepresenting.

 -John



On 6/9/11 6:23 AM, "David Matthews" <D.A.Matthews@bristol.ac.uk> wrote:

Dear Galaxy users,

I am trying to modify the human proteome based on my transcriptomeics data. In short I want to use my transcriptomics data to identify snps and from that identify coding changes that result from the snps. Ultimately I'd like to create a customised canonical proteome based on my transcriptomic data. Does anyone know how this might be done in Galaxy? I have started by running a pileup and so on but I am not a human geneticist (I am a virologist) so I may be making some fundamental errors!!

Any help is gratefully received!


Best Wishes,
David.

__________________________________
Dr David A. Matthews

Senior Lecturer in Virology
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Department of Cellular and Molecular Medicine,
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