[Biopython-dev] Re: [BioPython] GRAVY index program anyone?

[Yair Benita]

on 31/7/03 23:34, Iddo Friedberg at idoerg at burnham.org wrote:

> Hi,
> 
> Does anybody have a program which calculates a sequence's Grand average
> of hydropathicity (GRAVY)?
> 
> TIA,
> 
> ./I
> 
> 
Here is one of my functions. I have a collection of many protein analysis
functions, maybe its time to put together a module.
Yair 


# Kyte & Doolittle hydrophobiciy index
kd = { 'A': 1.8,'R':-4.5,'N':-3.5,'D':-3.5,'C': 2.5,
       'Q':-3.5,'E':-3.5,'G':-0.4,'H':-3.2,'I': 4.5,
       'L': 3.8,'K':-3.9,'M': 1.9,'F': 2.8,'P':-1.6,
       'S':-0.8,'T':-0.7,'W':-0.9,'Y':-1.3,'V': 4.2 }



# calculate the garvy according to kyte and doolittle.
def Gravy(ProteinSequence):
    
    if ProteinSequence.islower():
        ProteinSequence = ProteinSequence.upper()
        
    ProtGravy=0.0
    for i in ProteinSequence:
        ProtGravy += kd[i]
        
    return ProtGravy/len(ProteinSequence)


 
-- 
Yair Benita
Pharmaceutical Proteomics
Faculty of Pharmacy
Utrecht University