Difference between revisions of "Task 8 Lab Journal (MSUD)"

From Bioinformatikpedia
(Using PSSM)
(SIFT)
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=== SIFT ===
 
=== SIFT ===
  +
  +
SIFT was run on [http://sift.jcvi.org/www/SIFT_seq_submit2.html this server] with default parameters.
   
 
=== Polyphen2 ===
 
=== Polyphen2 ===

Revision as of 14:28, 27 June 2013

Analysis of evolutionary conservation of mutated positions

Using PSSM

A position-specific scoring matrix (PSSM) was created with PSI-Blast:

blastpgp -d /mnt/project/pracstrucfunc13/data/big/big_80 -i /mnt/home/student/weish/master-practical-2013/task01/refseq_BCKDHA_protein.fasta -j 5 -h 10e-10 -Q BCKDHA.pssm

The conservation (observed frequency) of the wildtype and mutant amino acids was extracted from the PSSM file with the following Python script:


<source lang=python> Extract amino acid frequencies from PsiBlast PSSM (created with -Q option).

Usage: python extract_aa_frequency.py <pssm file> [mutations]

Example for usage: python extract_aa_frequency.py BCKDHA.pssm P38H M82L T151M A222T C264W R265W R314Q R346H I361V Y413H

@author: Laura Schiller

import sys

pssm_file = open(sys.argv[1]) lines = pssm_file.readlines() pssm_file.close()

  1. positions of amino acid frequencies in PSSM

aa_position = { 'A': 22,

               'R': 23,
               'N': 24,
               'D': 25,
               'C': 26,
               'Q': 27,
               'E': 28,
               'G': 29,
               'H': 30,
               'I': 31,
               'L': 32,
               'K': 33,
               'M': 34,
               'F': 35,
               'P': 36,
               'S': 37,
               'T': 38,
               'W': 39,
               'Y': 40,
               'V': 41}

for i in range(2, len(sys.argv)):

   old_aa = sys.argv[i][0]
   new_aa = sys.argv[i][-1]
   position = sys.argv[i][1:(len(sys.argv[i]) - 1)]
   
   for j in range(2, len(lines)):
       splitted = lines[j].split()
       if splitted[0] == position:
           print("Frequencies at position %s: %s %s, %s %s" 
                 % (position, 
                    old_aa, 
                    splitted[aa_position[old_aa]], 
                    new_aa, 
                    splitted[aa_position[new_aa]]))
           break

</source>

Using MSA

Predicting effects of mutations

SIFT

SIFT was run on this server with default parameters.

Polyphen2

MutationTaster

SNAP