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.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, David. __________________________________ 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 Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk
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