<?xml version="1.0" encoding="utf-8"?>
<TEI xmlns="http://www.tei-c.org/ns/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:hal="http://hal.archives-ouvertes.fr/" xmlns:gml="http://www.opengis.net/gml/3.3/" xmlns:gmlce="http://www.opengis.net/gml/3.3/ce" version="1.1" xsi:schemaLocation="http://www.tei-c.org/ns/1.0 http://api.archives-ouvertes.fr/documents/aofr-sword.xsd">
  <teiHeader>
    <fileDesc>
      <titleStmt>
        <title>HAL TEI export of hal-02936276</title>
      </titleStmt>
      <publicationStmt>
        <distributor>CCSD</distributor>
        <availability status="restricted">
          <licence target="https://creativecommons.org/publicdomain/zero/1.0/">CC0 1.0 - Universal</licence>
        </availability>
        <date when="2026-05-18T07:16:35+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">IndelsRNAmute: Predicting deleterious multiple point substitutions and indels mutations</title>
            <author role="aut">
              <persName>
                <forename type="first">Alexander</forename>
                <surname>Churkin</surname>
              </persName>
              <idno type="halauthorid">1077857-0</idno>
              <affiliation ref="#struct-485539"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Yann</forename>
                <surname>Ponty</surname>
              </persName>
              <email type="md5">42fb37addd44a7405a61aa6c233dfb61</email>
              <email type="domain">lix.polytechnique.fr</email>
              <idno type="idhal" notation="string">yann-ponty</idno>
              <idno type="idhal" notation="numeric">3138</idno>
              <idno type="halauthorid" notation="string">2539307-3138</idno>
              <idno type="IDREF">https://www.idref.fr/113491611</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-7615-3930</idno>
              <affiliation ref="#struct-1051971"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Danny</forename>
                <surname>Barash</surname>
              </persName>
              <email type="md5">62fe82fe47eb90025177e0d75d1f6430</email>
              <email type="domain">cs.bgu.ac.il</email>
              <idno type="idhal" notation="numeric">1076993</idno>
              <idno type="halauthorid" notation="string">1029816-1076993</idno>
              <affiliation ref="#struct-300759"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Yann</forename>
                <surname>Ponty</surname>
              </persName>
              <email type="md5">42fb37addd44a7405a61aa6c233dfb61</email>
              <email type="domain">lix.polytechnique.fr</email>
            </editor>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2020-09-11 10:26:44</date>
              <date type="whenModified">2024-08-01 17:08:02</date>
              <date type="whenReleased">2020-09-11 14:43:43</date>
              <date type="whenProduced">2020-12-01</date>
              <date type="whenEndEmbargoed">2020-09-11</date>
              <ref type="file" target="https://inria.hal.science/hal-02936276v1/document">
                <date notBefore="2020-09-11"/>
              </ref>
              <ref type="file" subtype="author" n="1" target="https://inria.hal.science/hal-02936276v1/file/RNAMute_Evolved.pdf" id="file-2936276-2585126">
                <date notBefore="2020-09-11"/>
              </ref>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="117983">
                <persName>
                  <forename>Yann</forename>
                  <surname>Ponty</surname>
                </persName>
                <email type="md5">42fb37addd44a7405a61aa6c233dfb61</email>
                <email type="domain">lix.polytechnique.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-02936276</idno>
            <idno type="halUri">https://inria.hal.science/hal-02936276</idno>
            <idno type="halBibtex">churkin:hal-02936276</idno>
            <idno type="halRefHtml">&lt;i&gt;ISBRA 2020 - 16th International Symposium on Bioinformatics Research and Applications&lt;/i&gt;, Dec 2020, Moscow, Russia</idno>
            <idno type="halRef">ISBRA 2020 - 16th International Symposium on Bioinformatics Research and Applications, Dec 2020, Moscow, Russia</idno>
            <availability status="restricted">
              <licence target="https://about.hal.science/hal-authorisation-v1/">HAL Authorization<ref corresp="#file-2936276-2585126"/></licence>
            </availability>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="X">École polytechnique</idno>
            <idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno>
            <idno type="stamp" n="LIX" corresp="X">Laboratoire d'informatique de l'Ecole polytechnique</idno>
            <idno type="stamp" n="X-DEP-INFO">Département d'informatique de l’École polytechnique</idno>
            <idno type="stamp" n="IP_PARIS">Institut Polytechnique de Paris</idno>
          </seriesStmt>
          <notesStmt>
            <note type="audience" n="2">International</note>
            <note type="invited" n="0">No</note>
            <note type="popular" n="0">No</note>
            <note type="peer" n="1">Yes</note>
            <note type="proceedings" n="1">Yes</note>
          </notesStmt>
          <sourceDesc>
            <biblStruct>
              <analytic>
                <title xml:lang="en">IndelsRNAmute: Predicting deleterious multiple point substitutions and indels mutations</title>
                <author role="aut">
                  <persName>
                    <forename type="first">Alexander</forename>
                    <surname>Churkin</surname>
                  </persName>
                  <idno type="halauthorid">1077857-0</idno>
                  <affiliation ref="#struct-485539"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Yann</forename>
                    <surname>Ponty</surname>
                  </persName>
                  <email type="md5">42fb37addd44a7405a61aa6c233dfb61</email>
                  <email type="domain">lix.polytechnique.fr</email>
                  <idno type="idhal" notation="string">yann-ponty</idno>
                  <idno type="idhal" notation="numeric">3138</idno>
                  <idno type="halauthorid" notation="string">2539307-3138</idno>
                  <idno type="IDREF">https://www.idref.fr/113491611</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-7615-3930</idno>
                  <affiliation ref="#struct-1051971"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Danny</forename>
                    <surname>Barash</surname>
                  </persName>
                  <email type="md5">62fe82fe47eb90025177e0d75d1f6430</email>
                  <email type="domain">cs.bgu.ac.il</email>
                  <idno type="idhal" notation="numeric">1076993</idno>
                  <idno type="halauthorid" notation="string">1029816-1076993</idno>
                  <affiliation ref="#struct-300759"/>
                </author>
              </analytic>
              <monogr>
                <meeting>
                  <title>ISBRA 2020 - 16th International Symposium on Bioinformatics Research and Applications</title>
                  <date type="start">2020-12-01</date>
                  <settlement>Moscow</settlement>
                  <country key="RU">Russia</country>
                </meeting>
                <imprint/>
              </monogr>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <classCode scheme="halDomain" n="info.info-bi">Computer Science [cs]/Bioinformatics [q-bio.QM]</classCode>
              <classCode scheme="halTypology" n="COMM">Conference papers</classCode>
              <classCode scheme="halOldTypology" n="COMM">Conference papers</classCode>
              <classCode scheme="halTreeTypology" n="COMM">Conference papers</classCode>
            </textClass>
            <abstract xml:lang="en">
              <p>RNA deleterious point mutation prediction was previously addressed with programs such as RNAmute and MultiRNAmute. The purpose of these programs is to predict a global conformational rearrangement of the secondary structure of a functional RNA molecule, thereby disrupting its function. RNAmute was designed to deal with only single point mutations in a brute force manner, while in MultiRNAmute an efficient approach to deal with multiple point mutations was developed. The approach used in MultiRNAmute is based on the stabilization of the suboptimal RNA folding prediction solutions and/or destabilization of the optimal folding prediction solution of the wild type RNA molecule. The MultiRNAmute algorithm is significantly more efficient than the brute force approach in RNAmute, but in the case of long sequences and large m-point mutation sets the MultiRNAmute becomes exponential in examining all possible stabilizing and destabilizing mutations. Moreover, an inherent limitation in both programs is their ability to predict only substitution mutations, as these programs were not designed to work with deletion or insertion mutations. To address this limitation we herein develop a very fast algorithm, based on suboptimal folding solutions, to predict a predefined number of multiple point deleterious mutations as specified by the user. Depending on the user's choice, each such set of mutations may contain combinations of deletions, insertions and substitution mutations. Additionally, we prove the hardness of predicting the most deleterious set of point mutations in structural RNAs.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="institution" xml:id="struct-485539" status="VALID">
          <orgName>Shamoon Academic College of Engineering [Beer-Sheva]</orgName>
          <desc>
            <address>
              <addrLine>56 Bialik St. Beer-Sheva 84100</addrLine>
              <country key="IL"/>
            </address>
            <ref type="url">https://en.sce.ac.il/</ref>
          </desc>
        </org>
        <org type="researchteam" xml:id="struct-1051971" status="VALID">
          <orgName>Algorithms and Models for Integrative BIOlogy</orgName>
          <orgName type="acronym">AMIBIO</orgName>
          <date type="start">2018-01-01</date>
          <desc>
            <address>
              <addrLine>Laboratoire d'Informatique de l'École polytechniqueRoute de Saclay91128 Palaiseau CEDEX</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.lix.polytechnique.fr/amibio/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-2071" type="direct"/>
            <relation active="#struct-300340" type="indirect"/>
            <relation active="#struct-563936" type="indirect"/>
            <relation name="UMR7161" active="#struct-441569" type="indirect"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-300759" status="VALID">
          <idno type="IdRef">027957225</idno>
          <idno type="ISNI">0000000121828112</idno>
          <idno type="ROR">https://ror.org/05tkyf982</idno>
          <idno type="Wikidata">Q737332</idno>
          <orgName>Ben-Gurion University of the Negev</orgName>
          <orgName type="acronym">BGU</orgName>
          <desc>
            <address>
              <addrLine>P.O.B. 653 Beer-Sheva</addrLine>
              <country key="IL"/>
            </address>
            <ref type="url">http://in.bgu.ac.il/en/Pages/default.aspx</ref>
          </desc>
        </org>
        <org type="laboratory" xml:id="struct-2071" status="VALID">
          <idno type="IdRef">196509955</idno>
          <idno type="ISNI">0000000403673665</idno>
          <idno type="RNSR">200519331V</idno>
          <idno type="ROR">https://ror.org/04afed728</idno>
          <idno type="Wikidata">Q16009025</idno>
          <orgName>Laboratoire d'informatique de l'École polytechnique [Palaiseau]</orgName>
          <orgName type="acronym">LIX</orgName>
          <date type="start">2005-01-01</date>
          <desc>
            <address>
              <addrLine>1 Rue Honoré d’Estienne d’Orves, Bâtiment Alain Turing, 91120 Palaiseau</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.lix.polytechnique.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-300340" type="direct"/>
            <relation active="#struct-563936" type="indirect"/>
            <relation name="UMR7161" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-300340" status="VALID">
          <idno type="IdRef">027309320</idno>
          <idno type="ISNI">0000000121581279</idno>
          <idno type="ROR">https://ror.org/05hy3tk52</idno>
          <idno type="Wikidata">Q273626</idno>
          <orgName>École polytechnique</orgName>
          <orgName type="acronym">X</orgName>
          <date type="start">1794-03-11</date>
          <desc>
            <address>
              <addrLine>Route de Saclay, 91128 Palaiseau Cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.polytechnique.edu/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-563936" type="direct"/>
          </listRelation>
        </org>
        <org type="regroupinstitution" xml:id="struct-563936" status="VALID">
          <idno type="IdRef">238327159</idno>
          <idno type="ISNI">0000000502717600</idno>
          <idno type="ROR">https://ror.org/042tfbd02</idno>
          <idno type="Wikidata">Q48759778</idno>
          <orgName>Institut Polytechnique de Paris</orgName>
          <orgName type="acronym">IP Paris</orgName>
          <date type="start">2019-06-02</date>
          <desc>
            <address>
              <addrLine>Route de Saclay, 91120 Palaiseau Cedex, France</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.ip-paris.fr</ref>
          </desc>
        </org>
        <org type="regroupinstitution" xml:id="struct-441569" status="VALID">
          <idno type="IdRef">02636817X</idno>
          <idno type="ISNI">0000000122597504</idno>
          <idno type="ROR">https://ror.org/02feahw73</idno>
          <orgName>Centre National de la Recherche Scientifique</orgName>
          <orgName type="acronym">CNRS</orgName>
          <date type="start">1939-10-19</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.cnrs.fr/</ref>
          </desc>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>