software to locate given amino acid composition in sequence

hill at mcclb0.med.nyu.edu hill at mcclb0.med.nyu.edu
Sun Oct 27 07:13:26 EST 1991


In article <2C2D25732020D1AB at HELIX.MGH.HARVARD.EDU>,
KRAKOWER at BBRI.ERI.HARVARD.EDU writes:

> Does anyone know of a program (to run on a VAX or Mac) that could scan an 
> amino acid sequence and locate a region containing a given amino acid 
> composition? I have an amino acid composition of a proteolytic fragment and 
> want to quickly identify its location within the intact protein. Thank you.
> Terri Krakower, Ph.D.
> krakower at bbri.eri.harvard.edu

Terri,

If you have access to the GCG Sequence Analysis Software on your VAX,
it can do what you want although perhaps not in quite the fashion you
describe.  The PEPTIDESORT program will predict various proteolytic
digests of a given protein along with information about each peptide. 
The information for each peptide is by groups of amino acids (see
output at end of message), but you could also run the program without
any enzymes for each possible peptide to get its exact composition.

Other programs can probably do something similar, but GCG is the only
one I have "at my fingertips".

Good luck!

John
___________________________________________________________________________
John Edward Hill, Ph.D.            |  Department of Cell Biology             
Internet: HILL at MCCLB0.MED.NYU.EDU  |  New York University Medical Center
  EARN/Bitnet: HILL at NYUMED.BITNET  |  550 Fifth Avenue                  
212-263-7135    FAX: 212-263-8139  |  New York, New York  10016-6402
___________________________________________________________________________

P.S. Here's the description of the PEPTIDESORT program in GCG (version 7)
and a piece of an output file on a real protein:

************************************************************************
$ genhelp peptidesort description

PEPTIDESORT

  DESCRIPTION

         PEPTIDESORT  cuts  a  peptide  sequence   with  any  or  all  of  the
         proteolytic enzymes and reagents  from the public  or local data file
         ProEnzAll.Dat.  The peptides from each digest are sorted by position,
         weight, and retention time in a high-pressure liquid chromatograph at
         pH 2.1.   For each peptide  in each sorting, the  following  data are
         displayed:   beginning and  ending positions, molecular  weight, HPLC
         retention at  pH 2.1,  HPLC retention  at  pH 7.4, charge,  number of
         aromatic  residues,  number  of  acidic  residues,  number  of  basic
         residues, number of residues containing sulfur, number of hydrophilic
         residues,  and  number   of   hydrophobic  residues.    The  content,
         isoelectric point, and molar extinction coefficient at 280 nm of each
         peptide are shown with the table of peptides sorted by position.  The
         content can be displayed  in  the  order of  expected elution from an
         amino acid analyzer.
------------------------------------------------------------------------
$ eve Pet-B2.Pepsort

 PEPTIDESORT of: pet-b2.pep  check: 2769  from: 1  to: 327

 With Enzymes: TRYP
                         October 27, 1991  07:41  ..

               Digest with: Tryp.  Peptides Sorted by Position

 Pos  From     To   Mol Wt  Ret2.1  Ret7.4    Chg  Aro Acid Base Sulf Phil Phob
   1     1 -    3    376.5     7.2     7.6    1.0    0    0    1    1    1    2
   K1,M1,V1 Iso=9.67 Ext=0
   2     4 -   11    883.0    24.3    24.2    1.0    1    0    1    0    3    5
   G2,H1,K1,L1,S1,V1,W1 Iso=9.68 Ext=5690



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