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.


On 6/9/11 6:23 AM, "David Matthews" <d.a.matth...@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,

Dr David A. Matthews

Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol

Tel. +44 117 3312058
Fax. +44 117 3312091


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