<div dir="ltr"><div><div><div>Hi Jakub,<br><br></div>This might be a bit tangent to your question. If you want to just predict secondary structure from RNA sequence, you can try RNAStructure program, which is developed by David Mathew's lab. Here are the links for the web server and stand alone program download:<br><a href="http://rna.urmc.rochester.edu/RNAstructureWeb/">http://rna.urmc.rochester.edu/RNAstructureWeb/</a><br><a href="http://rna.urmc.rochester.edu/RNAstructure.html">http://rna.urmc.rochester.edu/RNAstructure.html</a><br><br></div>Good luck.<br><br></div>Ju<br><div><div><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Nov 28, 2014 at 7:41 PM, Jakub Stanislaw Nowak <span dir="ltr"><<a href="mailto:jakub.nowak@ed.ac.uk" target="_blank">jakub.nowak@ed.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hello everyone,<div><br><div>I am trying to model secondary structures of some RNA.</div><div><br></div><div>As I am not an expert in programming it is quite a challenge for me so far I found a way to access RNAfold from biopython via biomanycores.</div><div><br></div><div>I downloaded and installed both biomanycores and RNAfold tools in </div><div>/usr/local/bin/</div><div><br></div><div>and wrote a simple test script in python before loading my dataset</div><div><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><blockquote type="cite"><div>from Biomanycores import RNAFold</div><div><br></div><div>RNA = 'CUGCAUUGGCCAAAUUGGCCCUACUACGUAUGCUAGCAUGAGAUGUGACAGUACAGUGUACUUAC'</div><div><br></div><div>structure = RNAFold.execute(RNA)</div><div><br></div><div>print(structure)</div></blockquote></blockquote><div><br></div><div> </div><div>Unfortunately it hasn’t work and generated this error message:</div><div><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><blockquote type="cite">Traceback (most recent call last):</blockquote></div><div><blockquote type="cite"> File "/Users/user/Google Drive/Bioinformatics/smallRNAseq/Python secondary structure/RNAFoldtest", line 9, in <module></blockquote></div><div><blockquote type="cite"> structure = RNAFold.execute(RNA)</blockquote></div><div><blockquote type="cite"> File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Biomanycores-1.1210-py2.7.egg/Biomanycores/RNAFold.py", line 221, in execute</blockquote></div><div><blockquote type="cite"> handle, delta = rnafold_cmd.run(verbose=verbose)</blockquote></div><div><blockquote type="cite"> File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Biomanycores-1.1210-py2.7.egg/Biomanycores/AbstractCommandline.py", line 141, in run</blockquote></div><div><blockquote type="cite"> stderr=stderr_str)</blockquote></div><div><blockquote type="cite">ApplicationError: Non-zero return code 1 from '/usr/local/bin/RNAfold -f', message '/usr/local/bin/RNAfold: invalid option -- f'</blockquote></div></blockquote><br><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><blockquote type="cite">>>> </blockquote></div></blockquote><div><br></div>Do you know any solution for my problem? Alternatively maybe you know of some different approach to analyse secondary structure with biopython?<div><br></div><div>All best,</div><div><br></div><div>Jakub</div></div></div><br>The University of Edinburgh is a charitable body, registered in<br>
Scotland, with registration number SC005336.<br>
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