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Notes on application for codon usage / composition bias

 Incorporate JESS (functional site detection in
protein structures) from Thornton group into EMBOSS,
perhaps as an EMBASSY package.

Hi Jon

Here is the archive.

Unpack it...
$ tar zxvf Jess-1.1gamma.tar.gz
$ cd Jess-1.1gamma

Read the "documentation"...
$ less ReadMe.txt

Build it (requires expat lib)
$ ./build-jess $

Build an example template (from a legacy TESS template)
$ ./scripts/tess2jess data/example.tess > data/example.jess

Try it out...
$ ./jess -t data/example.jess -m data/pdb1tim.ent -d
delta=2.0 -f

I'm happy to hack it if need be, but I'll have to fit
it in around my
new job and the needs of a wife and two wee kiddies...

All the best


#### Follow up on Thornton-group software incorporation
into EMBOSS (7.)

"Jonathan Barker" 
"James Torrance" 
That's great. It might be a trivial job, e.g. just a few
questions by email, or more involved. Can't tell till I
take a look.



> Jon
> You may (or may not) know that I've just moved to the
systems group. I'm
> still settling in and not sure when I'll have time to
work on Jess.
> However, I will send you a copy of Jess, with
documentation (such as it
> is) under separate cover later today. If you could
take a look and tell
> me what I would need to do, I'd be able to estimate
when/if I could do it.
> BTW GPL suits me just fine.
> All the best
> Jonathan

Dear James, Jonathon, Janet

Thanks for the email James.

I'll gladly incorporate or help you incorporate Jess or
any other software
you have in your group. The restriction is that the
source would be made
available under the GPL license. The main advantage is
that your software
would be distributed widely and (like all the EMBOSS
apps) with potential
to be provided as a web service.

If you send me any stuff (code, documentation, test
data and examples etc)
you have I could take a look, or we could find a time
to talk about it,
whatever suits.



> Hello,
> At the Research Day, Jon and I spoke briefly about
EMBOSS. He indicated
> that there was some possibility of folding Jess into
the EMBOSS package.
> It strikes me that this would be a good way to make
Jess available now
> that it's harder for Jonathan Barker to support,
distribute and document
> it. I'm sending you all this email to help you all
get in contact with one
> another if this is something you want to pursue.
> Yours,
> James Torrance
> PhD Student
> European Bioinformatics Institute
> Wellcome Genome Campus
> Hinxton
> Cambridge
> CB10 1SD
> Phone: 01223 492549