[Biopython] random peptide sequences
ferreirafm at usp.br
ferreirafm at usp.br
Wed Apr 4 18:56:08 UTC 2012
Dear BioPython List,
I want to write a python script to generate random peptide sequences.
I have a scratch in my mind, however, I'm not sure how to deal with
data itself (like: use sequence or mutableSeq?). The problem is as
follow: I have a list of 20 string peptides which I join to produce a
sequence. I want to generate 1000+ sequences keeping the peptide1
(pep1) in a fix position (p1) and randomly permute (without
repetition) the remaining 19 peptides in the remaining 19 positions.
Repeat the first step keeping pep2 in a fix position p2 to generate
more 1000 peptides sequences. And repeat this step again and again for
all of the peptides & positions. At the end, I'm going to run a
function with each one of peptide sequences getting I binary result
like "positive" or "negative". What I have in mind is to randomly
generate 1000 peptide sequences of 19 peptides, insert pep1 at
position p1 in all of them; generate more 1000 peptide sequences of 19
peptides again and insert pep2 at position p2 in all of them; and so
on...At the end, I'm going to run the function for each of the
sequences and store results in a dict where value is the binary
result. Well, where Biopython goes? I'm completely new to Biopython
and would like to use it to solve the problem described. So, I'm
writing to ask you guys for some tips and advises to use Biopython
resources as much as possible. Any help is appreciated.
All the Best,
Fred
More information about the Biopython
mailing list