[Biopython] Biopython Digest, Vol 218, Issue 1

[Björn Johansson]

Hi, perhaps the easiest way is to generate all possible short sequences and
then finding them on the large sequence using str.find? Alternatively,
using some read mapper to place them on the reference sequence.

/bjorn



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ä ö
Björn Johansson, Assistant Professor
Department of Biology
University of Minho
Campus de Gualtar
4710-057 Braga
PORTUGAL
https://metabolicengineeringgroupcbma.github.io | www.bio.uminho.pt
Office +351-253 601517 | mob.  +351-967 147 704 | Dept secretary +351-253
60 4310


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>    1. Biopython RNA sequence mutation (Pierre-Damien Coureux)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 11 Mar 2021 17:54:56 +0100
> From: Pierre-Damien Coureux <pierre-damien.coureux at polytechnique.edu>
> To: biopython at biopython.org
> Subject: [Biopython] Biopython RNA sequence mutation
> Message-ID: <f615292a-dcb3-dc8f-e400-c5b42035f866 at polytechnique.edu>
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>
> Hello everyone
>
> I'm rather new to Biophython and I would greatly appreciate some help to
> write a clean script to fulfill my needs :
>
> The goal of my script is to align short RNA sequences that could
> complement with? one specific long RNA fragment
>
>
> My problem is that a G base in my short RNA fragment can complement with
> C or U bases in my long RNA fragment. The same for the U base that can
> complement with A or G bases.
>
> Thus, I would like to generate all the possible sequences from my short
> RNA fragment that could then complement with my long RNA fragment
>
>
> Here is an example : The initial sequence of my short RNA sequence is :
> AAUGCAGUGGG
>
> My reverse complement is CCCACUGCAUU and that sequence will be aligned
> with my long RNA fragment to find its target
>
> --> But I would like also to get all the possible combined mutated
> positions for Cs (into Us) and for As (into Gs) to search all targets in
> the long RNA fragment.
>
>
> I don't know if I should generate a matrix for the RNA sequence to allow
> mutation at specific position to generate all the sequences. Or should I
> extract only the bases that can me mutated and then recombine all the
> sequences obtained with bases that can not be mutated ? Which functions
> of python or biopython should I use for this purpose ?
>
> Well, any advice will be greatly appreciated
>
> Best regards
>
> Pierre-Damien
>
>
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