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    <p>Dear Peter,</p>
    <p><br>
    </p>
    <p>Thanks for pointing this out for me! The code snippets are very
      helpful!</p>
    <p><br>
    </p>
    <p>Best,</p>
    <p>Máté<br>
    </p>
    <div class="moz-cite-prefix">2023. 12. 15. 13:05 keltezéssel, Peter
      Cock írta:<br>
    </div>
    <blockquote type="cite" cite="mid:CAKVJ-_7uCZL_s35_E66EKTMmXUx6FAKyzLm+Do7Fpi7KJ2DdOg@mail.gmail.com">
      
      <div dir="ltr">
        <div>See also this discussion for proteins:<br>
        </div>
        <div><br>
        </div>
        <div><a href="https://github.com/biopython/biopython/issues/3636" moz-do-not-send="true" class="moz-txt-link-freetext">https://github.com/biopython/biopython/issues/3636</a></div>
        <div><br>
        </div>
        <div>Having the code handle RNA or DNA looks very
          straightforward in comparison (e.g. treating U and u the same
          as T and t in the C code).<br>
        </div>
        <div><br>
        </div>
        <div>Peter<br>
        </div>
      </div>
      <br>
      <div class="gmail_quote">
        <div dir="ltr" class="gmail_attr">On Fri, Dec 15, 2023 at
          10:33 AM 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>
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          <div>
            <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>2023. 12. 15. 10:16 keltezéssel, Peter Cock írta:<br>
            </div>
            <blockquote type="cite">
              <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" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">vaczy.foldi.mate@semmelweis.hu</a>>
                  wrote:<br>
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                <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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