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 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.Matthews@bristol.ac.uk

Hi David and John, If you send me your transcriptome data (I assume it's a GFF file), I can see if I can create a database from it. The version on galaxy shed is quite old. For this will have to use the latest development version, since there were many improvements on GFF parsing. I'm out of town (again) so I might be slow answering emails. Yours Pablo

P.S.: Why is that the standard annotations don't work for you? (just curious)

Sent from my iPad

On 2011-06-09, at 3:54 PM, David Matthews D.A.Matthews@bristol.ac.uk wrote:

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.ukx-msg://5/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 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.Matthews@bristol.ac.uk x-msg://5/D.A.Matthews@bristol.ac.uk