[Biopython] Biopython RNA sequence mutation

[Pierre-Damien Coureux]

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


-- 
L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
https://www.avast.com/antivirus