[BioPython] Transcription

[Michiel De Hoon]

It all depends on how you interpret the sequence that you give to the
transcribe function, and for that matter, to the translate function. For
translation, virtually all biological publications show the non-template
strand. Hence, the sequence given to the translate function in Biopython is
also interpreted as the non-template strand. For consistency, the sequence
given to the transcribe function in Biopython is also taken to be the
non-template strand:

>>> from Bio.Seq import *
>>> s = "ATGGTATAA"
>>> translate(s)
'MV*'
>>> transcribe(s)
'AUGGUAUAA'
>>> translate(_)
'MV*'

If you want to have the reverse complement, use the reverse_complement
function.

--Michiel.



Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032



-----Original Message-----
From: biopython-bounces at lists.open-bio.org on behalf of Michael Fahy
Sent: Tue 7/10/2007 9:36 PM
To: BioPython at lists.open-bio.org
Subject: [BioPython] Transcription
 
I just showed the BioPython tutorial to some of our Biology and Chemistry
faculty.  They pointed out that all the "Transcribe" function does is
replace each occurrence of "T" in the sequence with a "U".  The biologists
said that that is not what they mean by transcription.  They felt that each
nucleotide should have been replaced by the complementary nucleotide, and
that the resulting string should have been reversed.

This, they said, would be concordant with the way in which biologists use
the term "transcribe'.  It would not be hard to do, so why does BioPython do
what it does and call it transcription?

 

 

Michael Fahy

Mathematics and Computer Science

Chapman University

One University Drive

Orange, CA  92866

(714) 997-6879

fahy at chapman.edu

 

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