Any script that can produce different mutations of protein sequences at specified positions?
1
0
Entering edit mode
2.3 years ago
maa4618 • 0

Hello :)

I want to ask if there is a Python script or any other languages that can undergo the task shown below or something similar.

The task:

Input --> Wild-type (WT) protein sequence and indicate positions where you want mutations to occur.

Output --> Generate several sequences with different permutations using the 20 amino acids at these specific positions.

Thanks.

python sequences mutation • 2.7k views
ADD COMMENT
0
Entering edit mode

i know if we have any python script for this task. if you can post an example, i can look at it and provide some python code ideas how to do it.

ADD REPLY
0
Entering edit mode

I'll bite! what kind of ideas??

ADD REPLY
0
Entering edit mode

Yeah sure for example:

Input

  1. WT protein sequence: "MSQKQTPLKLNRFQGISIVAN"
  2. Want to mutate at position 2 and 4 from the sequence as denoted by X "MXQXQTPLKLNRFQGISIVAN"

The Output are mutated sequences at positions 2 and 4 with the 20 amino acids:

  • MAQAQTPLKLNRFQGISIVAN
  • MGQAQTPLKLNRFQGISIVAN
  • MAQGQTPLKLNRFQGISIVAN
  • MGQGQTPLKLNRFQGISIVAN
  • MFQPQTPLKLNRFQGISIVAN

There should be around 20^2 combinations

ADD REPLY
0
Entering edit mode

You can use rotkit.mutate in pyMOL. The basic command should be mutate(molecule,chain,resi,target,mutframe) .

ADD REPLY
1
Entering edit mode
2.3 years ago
Mensur Dlakic ★ 28k

Almost all protein design programs can do what you asked. Some of them are python-based, such as PyRosetta . There is also a server where you can try this program without investing time to learn its programming structure.

http://rosettadesign.med.unc.edu/

SCWRL4 can do quick "mutagenesis" by shuffling through residue rotamers from a predefined library.

ADD COMMENT
0
Entering edit mode

resettadesign server linked above appears to be no longer available.

ADD REPLY
0
Entering edit mode

Just looked into this - @Mensur is it subsumed by the PyRosetta Link above it?

ADD REPLY
1
Entering edit mode

I used the design server some years ago, but don't know why it doesn't work or if it migrated elsewhere. Without logging in, it seems that the main page is still there.

ADD REPLY
1
Entering edit mode

Interesting. The server was not working when I checked earlier but it seems to be now.

ADD REPLY
0
Entering edit mode

sorry for adding to the confusion gentlemen. on the bright side, i did not know it existed and will now go play with it :-D

ADD REPLY

Login before adding your answer.

Traffic: 1642 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6