Proteolysis Of A Protein Sequence

Question

[Sandy Abs]

Can any one help me for a python script to break the protein sequences by enzymatic action.( trypsin, etc). If trypsin breaks protein sequences at K and R, can i have a script for getting all the peptide fragments after cutting.. at K and R for a sequence.

[Neilfws]

I removed the tag "restriction" from question; restriction enzymes are nothing to do with proteolytic cleavage.

[Jdnavarro]

What's your input file? FASTA?

[Fess]

I just developed one today for the same problem. If you still the python script on trypsin_digest you email me [e-mail]

Answer 1

[Prateek]

Have a look at this http://www.expasy.ch/tools/peptidecutter/

Answer 2

[Dawe]

There should be a plenty of such scripts. BTW, you can look at function "cleave" (line 764) in this source

http://code.google.com/p/nsilk/source/browse/trunk/xllib/sequence.py?r=143

Nsilk is a python tool to spot protein-protein interactions, but that function will predict peptides from a sequence. You only have to be inspired as it uses some classes and objects that you won't have.

d

Answer 3

[Mark Evans]

This is pretty simple to do with python, no fancy scripts are required.

>>> protein = 'MLTFKFYLPKQATELKDLQCLEDELGPLRHVLDLTESKSFQLEDAENFIS'
>>> 
>>> print protein.replace('K','-').replace('R','-').split('-')
['MLTF', 'FYLP', 'QATEL', 'DLQCLEDELGPL', 'HVLDLTES', 'SFQLEDAENFIS']

You can plug this in anywhere in your program.

You could make the code a bit more dynamic I suppose by using a dictionary to hold the enzyme:recognition site combinations and building the command that way, rather than hardwiring it.

Answer 4

[Neilfws]

I'd start with a tool designed for this purpose. One option is digest, from the EMBOSS suite of programs.

It should not be too difficult to integrate this tool into a Python script, either by calling it and parsing the output, or running the EMBOSS tool independently then parsing. I believe that BioPython has some options for working with EMBOSS via the Bio.Emboss.Applications module.

[Sandy Abs]

Thats what i am asking for.. I couldnt get that exactly. If possible. Can you do it and reply??