<div dir="ltr"><div class="gmail_default" style="font-family:monospace;font-size:small">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.</div><div class="gmail_default" style="font-family:monospace;font-size:small"><br></div><div class="gmail_default" style="font-family:monospace;font-size:small">/bjorn</div><div class="gmail_default" style="font-family:monospace;font-size:small"><br></div><div class="gmail_default" style="font-family:monospace;font-size:small"><br></div><div class="gmail_default" style="font-family:monospace;font-size:small"><br></div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><font face="garamond, serif" size="2">______O_________oO________oO______o_______oO__</font><span style="font-family:garamond,serif">______O_________oO________ </span><font face="garamond, serif" size="2">å ä ö<br>Björn Johansson, Assistant Professor<br>Department of Biology<br>University of Minho<br>Campus de Gualtar<br>4710-057 Braga<br>PORTUGAL</font></div><div dir="ltr"><font face="garamond, serif" size="2"><a href="https://metabolicengineeringgroupcbma.github.io" target="_blank">https://metabolicengineeringgroupcbma.github.io</a> | <a href="http://www.bio.uminho.pt" target="_blank">www.bio.uminho.pt</a></font><div><font face="garamond, serif" size="2">Office +351-253 601517 | mob. +351-967 147 704 | </font><font face="garamond, serif" size="2">Dept secretary +351-253 60 4310</font></div></div></div></div></div></div></div></div></div></div></div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Mar 12, 2021 at 5:00 PM <<a href="mailto:biopython-request@biopython.org">biopython-request@biopython.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send Biopython mailing list submissions to<br>
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Today's Topics:<br>
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1. Biopython RNA sequence mutation (Pierre-Damien Coureux)<br>
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----------------------------------------------------------------------<br>
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Message: 1<br>
Date: Thu, 11 Mar 2021 17:54:56 +0100<br>
From: Pierre-Damien Coureux <<a href="mailto:pierre-damien.coureux@polytechnique.edu" target="_blank">pierre-damien.coureux@polytechnique.edu</a>><br>
To: <a href="mailto:biopython@biopython.org" target="_blank">biopython@biopython.org</a><br>
Subject: [Biopython] Biopython RNA sequence mutation<br>
Message-ID: <<a href="mailto:f615292a-dcb3-dc8f-e400-c5b42035f866@polytechnique.edu" target="_blank">f615292a-dcb3-dc8f-e400-c5b42035f866@polytechnique.edu</a>><br>
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<br>
Hello everyone<br>
<br>
I'm rather new to Biophython and I would greatly appreciate some help to <br>
write a clean script to fulfill my needs :<br>
<br>
The goal of my script is to align short RNA sequences that could <br>
complement with? one specific long RNA fragment<br>
<br>
<br>
My problem is that a G base in my short RNA fragment can complement with <br>
C or U bases in my long RNA fragment. The same for the U base that can <br>
complement with A or G bases.<br>
<br>
Thus, I would like to generate all the possible sequences from my short <br>
RNA fragment that could then complement with my long RNA fragment<br>
<br>
<br>
Here is an example : The initial sequence of my short RNA sequence is : <br>
AAUGCAGUGGG<br>
<br>
My reverse complement is CCCACUGCAUU and that sequence will be aligned <br>
with my long RNA fragment to find its target<br>
<br>
--> But I would like also to get all the possible combined mutated <br>
positions for Cs (into Us) and for As (into Gs) to search all targets in <br>
the long RNA fragment.<br>
<br>
<br>
I don't know if I should generate a matrix for the RNA sequence to allow <br>
mutation at specific position to generate all the sequences. Or should I <br>
extract only the bases that can me mutated and then recombine all the <br>
sequences obtained with bases that can not be mutated ? Which functions <br>
of python or biopython should I use for this purpose ?<br>
<br>
Well, any advice will be greatly appreciated<br>
<br>
Best regards<br>
<br>
Pierre-Damien<br>
<br>
<br>
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</blockquote></div>