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FAQ: Bioinformatics
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Bioinformatics FAQ

There are a large number of bioinformatics programs available to CBRG account holders via this web site. These examples (Frequently Asked Questions) are used to illustrate the use of these tools in answering typical queries posed by researchers.

The major web-based tools from the CBRG are listed, here.


What is the molecular weight/codon frequency of my protein?

Program name: pepstats     

(molbiol username / password required)

Example output from pepstats

     Molecular weight = 138771.48 		Residues = 1214  
     Average Residue Weight  = 114.309 	Charge   = 20.0  
     Isoelectric Point = 8.5752
     A280 Molar Extinction Coefficient  = 100420  
     A280 Extinction Coefficient 1mg/ml = 0.72      
     Improbability of expression in inclusion bodies = 0.675     
     Residue		Number		Mole%		DayhoffStat
     A = Ala		72		5.931  		0.690  	
     B = Asx		0		0.000  		0.000  	
     C = Cys		15		1.236  		0.426  	
     D = Asp		80		6.590  		1.198  	
     E = Glu		99		8.155  		1.359  	
     F = Phe		35		2.883  		0.801  	
     G = Gly		60		4.942  		0.588  	
     H = His		20		1.647  		0.824  	
     I = Ile		64		5.272  		1.172  	
     K = Lys		91		7.496  		1.136  	
     L = Leu		109		8.979  		1.213  	
     M = Met		40		3.295  		1.938  	
     N = Asn		39		3.213  		0.747  	
     P = Pro		68		5.601  		1.077  	
     Q = Gln		53		4.366  		1.119  	
     R = Arg		98		8.072  		1.647  	
     S = Ser		76		6.260  		0.894  	
     T = Thr		74		6.096  		0.999  	
     V = Val		77		6.343  		0.961  	
     W = Trp		10		0.824  		0.634  	
     X = Xaa		0		0.000  		0.000  	
     Y = Tyr		34		2.801  		0.824  	
     Z = Glx		0		0.000  		0.000 
     Property	Residues		Number		Mole%
     Tiny	(A+C+G+S+T)		297		24.465
     Small	(A+B+C+D+G+N+P+S+T+V)	561		46.211
     Aliphatic	(I+L+V)			250		20.593
     Aromatic	(F+H+W+Y)		99		 8.155
     Non-polar	(A+C+F+G+I+L+M+P+V+W+Y)	584		48.105
     Polar	(D+E+H+K+N+Q+R+S+T+Z)	630		51.895
     Charged	(B+D+E+H+K+R+Z)		388		31.960
     Basic	(H+K+R)			209		17.216
     Acidic	(B+D+E+Z)		179		14.745

Further reading: pepstats background


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This file last modified Friday March 09, 2007