Extinction Coefficient

Christopher Blencowe cbb at convex.phazc.uni-heidelberg.de
Thu Jun 29 04:09:55 EST 1995


: I don't have a program but it's so easy that you may not need one.
: Check the following ref: Gill and von Hippel Anal Biochm 182:319-326 (1989)

Fine, i just hacked in such a program, needs a gawk or mawk or nawk
text processor, e.g. for MS-DOS on SIMTEL/awk

The input is a one letter protein sequence in fasta format
(one line header, rest are sequence lines)
Given into the PD for you !


#!/usr/local/bin/gawk -f
#
# protein_absorbtion
#
# (c) 1995 Christopher Blencowe (cbb at convex.phazc.uni-heidelberg.de)
#
# estimate the molar extinction coefficent at 280nm per cm of a given
# protein sequence in one letter code, one line of header (fasta)
# according to 
# Gill and von Hippel Anal Biochm 182:319-326 (1989)
# 
# estimated error around 5%

BEGIN{
# read the header
getline
header=$0
seq=""
tyr=0
trp=0
cys=0
}

{
seq=seq toupper($0)
}

END{
gsub(" ","",seq)
for (i=1;i<=length(seq);i++){
	aa=substr(seq,i,1)
	if (aa=="C") cys++
	if (aa=="W") trp++
	if (aa=="Y") tyr++
	}

e=1280*tyr + 5690*trp + 120*cys

print header
print "Extinktion coefficent 280nm [1/(Mol*cm)]: " e
print "Number of AA:  " length(seq)
print "Number of Cys: " cys
print "Number of Trp: " trp
print "Number of Tyr: " tyr
}
# EOF


--
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>			Christopher Blencowe		 _______     <
>>	 ||	Pharmazeutisch-Chemisches Institut	| .._.. |   <<
>>>	/  \	      Universitaet Heidelberg		|_______|  <<<
>>     /____\ 		      GERMANY			/______/    <<
>		cbb at convex.phazc.uni-heidelberg.de        	     <
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