Re[2]: AA composition, (was blank)

Tim_Slattery@berlex.com
Mon, 9 Feb 1998 09:24:28 -0800

I must have missed the original post (it is hard to think while
treading water :-) ).

The Peptidesort program of GCG will give you an amino acid composition
both as number of each AA and as mole %.

It has been too many years since I used GCG so I can't remember the
syntax for the command, but, that should get you started.

These days I use GPMAW to get compositions.

--tks

Weather: the first sun in days, if not weeks. Yea!

Tim Slattery
Protein Biochemistry and Biophysics Department
Berlex Biosciences
tim_slattery@berlex.com


______________________________ Reply Separator _________________________________
Subject: Re: AA composition, (was blank)
Author: p_morrison@dfci.harvard.edu at Internet
Date: 2/7/98 10:15 AM

Laurey Steinke wrote:
>
> Hello all, Is there a way to get an amino acid analysis composition in
> molar % for known proteins (without sitting down and counting the amino
> acids and doing a tally?) I have gcg but can't seem to find such a thing.

Laurey,

Not positive if this is the number you want but you can take the codon
usage tables that Mike Cherry generated in '92 using GCG found here:

ftp://ftp.ebi.ac.uk/pub/databases/codonusage/

and then just tally the codons to amino acid. Taking the easiest one
codon amino acid trp in humans you get:

AmAcid Codon Number /1000 Fraction ..
Trp TGG 8820.00 14.74 1.00

or % 1.47 of the AA's in human are trp.

Mike did it in 1992 but I would bet the drift since the genome explosion
would not be significant for the animals in these tables with a large
number of genes in the table in '92.
Then again someone should have a more current table out on the web with
codons already tallied.

hope this helps, Paul

weather: shiny coat of ice.

Paul Morrison
Molecular Biology Core Facilities
Dana-Farber Cancer Institute
44 Binney Street
Boston MA, 02115

p_morrison@dfci.harvard.edu
http://mbcf.dfci.harvard.edu