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!
On 9 Jun 2011, at 19:18, John David Osborne wrote:
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.Matthews(a)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!
Dr David A. Matthews
Senior Lecturer in Virology
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University of Bristol
Tel. +44 117 3312058
Fax. +44 117 3312091