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:
> 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
> BS8 1TD
> Tel. +44 117 3312058
> Fax. +44 117 3312091
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