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Bio::SeqUtils::ProtParam::ProteinAnalysis Class Reference

List of all members.


Detailed Description

This class contains methods for protein analysis.  The class init method takes
only one argument, the protein sequence as a string and build a sequence
object using the Bio.Seq module. This is done just to make sure the sequence
is a protein sequence and not anything else.

methods:

count_amino_acids:

Simply counts the number times an amino acid is repeated in the protein
sequence. Returns a dictionary {AminoAcid:Number} and also stores the
dictionary in self.amino_acids_content.

get_amino_acids_percent:

The same as count_amino_acids only returns the Number in percentage of entire
sequence. Returns a dictionary and stores the dictionary in
self.amino_acids_content_percent.

molecular_weight:
Calculates the molecular weight of a protein.

aromaticity:

Calculates the aromaticity value of a protein according to Lobry, 1994. It is
simply the relative frequency of Phe+Trp+Tyr.


instability_index:

Implementation of the method of Guruprasad et al. (Protein Engineering
4:155-161,1990). This method tests a protein for stability. Any value above 40
means the protein is unstable (=has a short half life). 

flexibility:
Implementation of the flexibility method of Vihinen et al. (Proteins. 1994 Jun;19(2):141-9).

isoelectric_point:
This method uses the module IsoelectricPoint to calculate the pI of a protein.

secondary_structure_fraction:
This methods returns a list of the fraction of amino acids which tend to be in Helix, Turn or Sheet.
Amino acids in helix: V, I, Y, F, W, L.
Amino acids in Turn: N, P, G, S.
Amino acids in sheet: E, M, A, L.
The list contains 3 values: [Helix, Turn, Sheet].


protein_scale(Scale, WindwonSize, Edge):

An amino acid scale is defined by a numerical value assigned to each type of
amino acid. The most frequently used scales are the hydrophobicity or
hydrophilicity scales and the secondary structure conformational parameters
scales, but many other scales exist which are based on different chemical and
physical properties of the amino acids.  You can set several  parameters that
control the computation  of a scale profile, such as the window size and the
window edge relative weight value.  WindowSize: The window size is the length
of the interval to use for the profile computation. For a window size n, we
use the i- ( n-1)/2 neighboring residues on each side of residue it compute
the score for residue i. The score for residue is  the sum of the scale values
for these amino acids,  optionally weighted according to their position in the
window.  Edge: The central amino acid of the window always has a weight of 1.
By default, the amino acids at the remaining window positions have the same
weight, but  you can make the residue at the center of the window  have a
larger weight than the others by setting the edge value for the  residues at
the beginning and end of the interval to a value between 0 and 1. For
instance, for Edge=0.4 and a window size of 5 the weights will be: 0.4, 0.7,
1.0, 0.7, 0.4.  The method returns a list of values which can be plotted to
view the change along a protein sequence.  Many scales exist. Just add your
favorites to the ProtParamData modules.

Definition at line 10 of file ProtParam.py.


Public Member Functions

def __init__
def aromaticity
def count_amino_acids
def flexibility
def get_amino_acids_percent
def gravy
def instability_index
def isoelectric_point
def molecular_weight
def protein_scale
def secondary_structure_fraction

Public Attributes

 amino_acids_content
 amino_acids_percent
 length
 sequence

Private Member Functions

def _weight_list

The documentation for this class was generated from the following file:

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