codon usage in sea urchins

Will Fischer wmf%caat at LANL.GOV
Tue Nov 20 19:21:00 EST 1990


I previously asked

>>Can anyone out there point me to a table of codon usages for
>>SEA URCHIN EGGS?  For that matter, how about a good public-domain
>>or shareware program for generating same?

Don Gilbert said

>It just so happens that I made a sea urchin codon table for
>people at iu.  You can get it from anon. ftp to iubio.bio.indiana.edu,
>cd [archive.molbio.data], get SEA-URCHIN.CODON-GCG.
>
>I had a codon table maker hacked from GCG software but it broke with
>the new feature table format of GenBank. 

Mark Gunnell generated and sent tables:

>  I've enclosed three codonfrequency tables generated by the GCG program
>CodonFrequency.  These sequences were initially found in by scanning several 
>nucleotide databases [GenBank-65,EMBL-24,PirNuc-36], with DocSearch, a string 
>matching program, looking for the terms "Coding" or "CDS" and "Sea" and 
>"Urchin" and "Egg".

Michael Gribskov asked in response:
>It will be easier to respond to this question if we can get a little 
>more detail.  For instance, what kind of sea urchin?
> ...
>Are you interested in overall codon usage, or usage of highly expressed 
>genes?  Are you interested in codon usage of genes expressed only
>in early development (i.e. eggs), or at any time in the life cycle?

First, the disclaimer -- I got this request from "outside" my workplace
(GenBank), and posted this note hoping to get a response so I could give
these people *some* help.  I have since found out more about the question...

A researcher (haven't asked if I can name him, so I won't) isolated a
peptide from Strongylocentrotus purpuratus eggs.  Apparently it is expressed
in other tissues as well, and in other organisms.  Having partially sequenced
the peptide, he wanted to synthesize oligos for PCR primers...
I don't know what the best approach would be, other than using just the
known S.purpuratus egg codons to generate the primers; if there are other
opinions out there, I'd like to hear them (I am NO wet-bench biologist).

Thanks to those who replied, if anyone else cares to, thanks in advance.

-- Will Fischer

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