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<p>Dear Peter,</p>
<p><br>
</p>
<p>Thank thank you very much for the suggestion! I will go ahead
with this method.</p>
<p><br>
</p>
<p>Best wishes,</p>
<p>Máté<br>
</p>
<div class="moz-cite-prefix">2023. 12. 15. 10:16 keltezéssel, Peter
Cock írta:<br>
</div>
<blockquote type="cite" cite="mid:CAKVJ-_5x+BAgCZRjHe2DkK3J67+Z3jWMM49uQCaOaPfMLCTk_A@mail.gmail.com">
<div dir="ltr">
<div>Hello Máté,</div>
<div><br>
</div>
<div>I see you are referring to the
PositionSpecificScoringMatrix class</div>
<div>defined in Bio/motifs/matrix.py which does indeed appear to
be DNA</div>
<div>only. I can't comment on any drawbacks in generalizing that
code</div>
<div>(I can see how I would attempt this), but your first idea
is what I would</div>
<div>have suggested in the short term - map any U to T in your
motifs and</div>
<div>sequences to be searched (i.e. treat as DNA).<br>
</div>
<div><br>
</div>
<div>Peter<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Dec 14, 2023 at
4:18 PM Váczy-Földi Máté <<a href="mailto:vaczy.foldi.mate@semmelweis.hu" moz-do-not-send="true" class="moz-txt-link-freetext">vaczy.foldi.mate@semmelweis.hu</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">
<div>
<p>Dear Mailing List Members,</p>
<p><br>
</p>
<p>I would like to ask a question related to the Bio.motifs
package.<br>
</p>
<p>I am currently working a project where I need to find RNA
motifs in RNA sequences. After consideration we have
decided to search for the motif occurrences using PSSMs,
and I would like to implement this using Biopython. I
looked at the relevant codes in the in the matrix.py file
and I have seen that the PSSM calculate method is hard
coded to work only with DNA. There is also a note saying
"the sequence can only be a DNA sequence". <br>
</p>
<p>My question is that:</p>
<ol>
<li>Would it be safe to replace all Us with Ts in the
sequences/PSSMs and run the search that way? (I have
seen one example of someone doing this while searching.)<br>
</li>
<li>Or would it be possible for me to modify the code to
work with RNA by replacing the Ts with Us in the code
(or in a more sophisticated way providing an option for
both)?</li>
</ol>
<p>For the latter I understand that I have to modify the
_pwm.c code too. I am not experienced in C, but what I
gathered by looking at that code, it should not be a big
problem.</p>
<p>I am just looking for some confirmation that I am not
overlooking some computational or biology related reason
why the above mentioned solutions are not possible.</p>
<p><br>
</p>
<p>Thank you in advance for your kind help!</p>
<p><br>
</p>
<p>Best wishes,</p>
<p>Máté Váczy-Földi<br>
</p>
</div>
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</blockquote>
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</blockquote>
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