Difference between revisions of "Task 8 Lab Journal (MSUD)"
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− | The conservation (observed frequency) of the wildtype and mutant amino acids was extracted from the PSSM file with the following Python script: |
+ | The conservation (observed frequency) of the wildtype and mutant amino acids was extracted from the PSSM file with the following Python script (located at <code>/mnt/home/student/schillerl/MasterPractical/task8/extract_aa_frequency.py</code>): |
Revision as of 15:09, 27 June 2013
Contents
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 (located at /mnt/home/student/schillerl/MasterPractical/task8/extract_aa_frequency.py
):
<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()
- 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
This server was used with default parameters to run Polyphen2.