Proteolysis Of A Protein Sequence
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11.8 years ago
Sandy Abs ▴ 10

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.

enzyme python • 3.9k views
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I removed the tag "restriction" from question; restriction enzymes are nothing to do with proteolytic cleavage.

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What's your input file? FASTA?

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I just developed one today for the same problem. If you still the python script on trypsin_digest you email me ifess.fes@gmail.com

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11.8 years ago
Prateek ★ 1.0k

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

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11.8 years ago
Dawe ▴ 270

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

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11.6 years ago
Mark Evans ▴ 50

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.

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11.8 years ago
Neilfws 49k

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.

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

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