Codon Usage Analysis

Keith Robison robison1 at husc10.harvard.edu
Thu Jul 16 14:46:59 EST 1992

lmh at medg.lcs.mit.edu (Minghsun Liu) writes:

>I am not sure if this is the right newsgroup to post too.  And
>comments will be appreciated.

>Recently, I was given the task of doing a codon usage analysis on
>pseudomonas putida.  Except access to the net, I really don't have
>much resources here.  (I am remotely logged in.)  My quesrtion is, as
>a novice, what particular points should I look out for.  (I am
>planning to pull out the data in GenBank and write a program to parse
>and anlyze the data.)  Orr better yet, has there been an analysis like
>this done?

>Many thanx in advance!

>- Minghsun Liu

	I have UNIX software which will accomplish this, but at this time
it requires a local copy of GenBank and software to access it
(i.e. GCG or Eugene).    
	Generating the data takes very little effort once you have
a set of entries culled of duplicates.  I would be happy to generate
the table if you are willing to cull the CDS list.

Keith Robison
Harvard University
Program in Biochemistry, Molecular, Cellular, and Developmental Biology

robison at ribo.harvard.edu 

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