IUBio

profiles from prosite to GCG ??

Ewan Birney birney at sanger.ac.uk
Mon Oct 21 07:59:04 EST 1996


iribhn wrote:
> 
> Hello,
> 
> I'd like to retrieve profile matrixes from Prosite and use them
> in GCG programs (e.g. findpatterns). The only problem is that the
> format are not compatible. Does anybody knows a "translater" that
> can convert a Prosite profile matrix into a GCG profile matrix ?
> 
> Thanks in advance,

Well.. 

The point is that the extended profiles in Prosite have more 
information than the current "gcg style" profiles. I have some
code that does an approximate conversion, but it is not suggested
as the best way to do it.

currently I am switching over all my work (PairWise and SearchWise)
to run using extended profile formats and HMMs from HMMer: so,
if you wait a couple of months...

I could make a little converter program now. What is the need for
this (does prosite provide something at the moment?)

ewan



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