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Notes on application for codon usage / composition bias

 Awaiting more details on this one ... :
Subject: [emboss-bug] Replacement for Plotsimilarity
From: "Peter Rice" 
Date: Thu, March 2, 2006 12:09 pm
To: a.r.hoelzel@durham.ac.uk
Cc: "emboss-bug@emboss.open-bio.org"

Priority: Normal
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Dear Rus,

Hamish McWilliam passed on your request (attached
below) to us in the EMBOSS team.

Can you fill us in on what you "really need" ... for
example the kind of score
you would like to plot, and some example alignments.

Personally, I was never quite satisfied with the score
PlotSimilarity used.

EMBOSS has several algorithms for calculating the
consensus (in prettyplot for
example) which we could adapt and use to calculate
scores for a plot.


Peter Rice

>>Date: Wed, 1 Mar 2006 17:48:30 +0000
>>From: a.r.hoelzel@durham.ac.uk
>>To: support@ebi.ac.uk
>>Subject: Re: EBI HELP: OTHER (a.r.hoelzel@dur.ac.uk)
(duggan) (SUP#303899)
>>Hi, yes it would be great to have something similar
in EMBOSS - please feel
>>free to pass my details on to the relevant people.
Thanks, Best, Rus
>> Quoting support@ebi.ac.uk:
>>>> Great - thanks for that - it was PLOTSIMILARITY
for sure. Best, Rus
>>> Okay that helps. I've asked around and we don't
know of any other programs
>>> that offer the same functionality as
PLOTSIMILARITY. However I've talked to
>>> one of the EMBOSS developers and they think thay
may be able to put
>>> together something to do the same job.
>>> If you are interested in seeing something sililar
in EMBOSS you can get
>>> back to me and I can pass your details on to the
EMBOSS folks, or you
>>> can ask the question on the EMBOSS mailing list
>>> (emboss@emboss.open-bio.org).