Open Reading Frame And Codons

Question

[Wilmer Garzon]

How I can find the ORF in a sequence using Python? also I need find all codons.

Thanks.

Answer 1

[Nikolay Vyahhi]

List of all codons:

genome = 'ACGTACGT....'
print map(lambda x: ''.join(x), zip(genome[0:], genome[1:], genome[2:]))

Set of all codons:

genome = 'ACGTACGT....'
print set(map(lambda x: ''.join(x), zip(genome[0:], genome[1:], genome[2:])))

If your genome is large, use itertools.izip instead of zip:

import itertools
itertools.izip(genome[0:], genome[1:], genome[2:])

To find ORF it's better to use Biopython (see zev.kronenberg's link).

[Nikolay Vyahhi]

If you genomes are large, use itertools.izip instead of zip: import itertools; itertools.izip(genome[0:], genome[1:], genome[2:])

Answer 2

[Zev.Kronenberg]

Googled:

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc224

Answer 3

[Wilmer Garzon]

Thanks,

I worked with the fasta file NC_005816.fna following the steps indicated in (http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc224), but if I compare this ORF's with the obtained using toolbox WEB of NCBI http://www.ncbi.nlm.nih.gov/projects/gorf/orfig.cgi the results are differents, why?

I need to use python because the file of my sequence is 4GB. I can't use NBCI toolbox.

Thanks.

[Michael]

would be more appropriate as a comment. possible reason for difference: different genetic codes.