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
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".
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 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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