[BioPython] back-translation method for Seq object?
Bruce Southey
bsouthey at gmail.com
Wed Oct 22 21:02:18 UTC 2008
Hi,
Some of the neat things about Python is how easy it is to modify your
own code and adapt others code into yours.
So here is some code (under the BSD license) that may be useful on
this. This is a simple back or reverse translation code with many of the
things that I have been 'talking' about. This should be self-contained
and works on Linux system with Python2.3+. It is oriented around an
peptide sequence 'AFLFQPQRFGR' but hopefully is more general (I have not
tested that).
a) Convert an amino acid sequence into both a regular expression or DNA
sequence involving ambiguous codes. There are functions to convert the
regular expression or DNA sequence involving ambiguous codes back to a
protein sequence since neither of these are standard.
b) Regular expression search on a list of sequences in fasta format.
c) Obtain all possible DNA sequences from an regular expression form of
the amino acid sequence. Obviously this is very large as for the above
sequence there are 442368 combinations (but Python is fairly quick...
about 10 seconds on my opteron 270 system bogomips =3991.08)
Enjoy
Bruce
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