[BioPython] Transcription

[Martin MOKREJŠ]

BTW, someone who has the rights should include this example in the docs.
The relevant section is empty: http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc68

Martin


Michiel De Hoon wrote:
> 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 nucleotide should have been replaced by the complementary nucleotide, and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
> 
>  
> 
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
> 
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
> 
> 

-- 
Dr. Martin Mokrejs
Dept. of Genetics and Microbiology
Faculty of Science, Charles University
Vinicna 5, 128 43 Prague, Czech Republic
http://www.iresite.org
http://www.iresite.org/~mmokrejs