[ensembl-dev] transform swissprot protein coordinates into genome coordinates
Stéphane Plaisance
stephane.plaisance at vib.be
Fri Aug 31 15:39:36 BST 2012
Dear All,
I have downloaded the PFAM full list for mm9 and would like to obtain the genomic coordinates for each record (from cols 2+3 below )
Is there someone with recyclable code for doing so?
My input is in Swissprot format (relative to ATG in the relative Acc as shown below
> #Pfam-A regions from Pfam version 26.0 for ncbi taxid 10090 'Mus musculus (strain C57BL/6)'
> #Total number of proteins in proteome: 47211
> #<seq id> <alignment start> <alignment end> <envelope start> <envelope end> <hmm acc> <hmm name> <type> <hmm start> <hmm end> <hmm length> <bit score> <E-value> <clan>
> Q9JKB1 5 215 5 216 PF01088 Peptidase_C12 Domain 1 213 214 271.10 4.6e-78 CL0125
> E9Q751 46 129 46 129 PF04822 Takusan Family 1 84 84 96.90 4.5e-25 No_clan
> D3YVR1 2 161 2 161 PF00743 FMO-like Family 1 160 532 325.60 4.1e-94 CL0063
> B1AQR8 223 351 223 352 PF00337 Gal-bind_lectin Domain 1 132 133 134.30 1.6e-36 CL0004
this looks feasible and probably needs some external ref and slice magic, I have not used this for several years now and am a bit rusted
Thanks for any piece of code to start with
Stephane
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