Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases
Identifieur interne : 000281 ( Pmc/Checkpoint ); précédent : 000280; suivant : 000282Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases
Auteurs : Marco Pellegrini [Italie] ; Maria Elena Renda [Italie] ; Alessio Vecchio [Italie]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2012.
Abstract
Tandem repeats are multiple duplications of substrings in the DNA that occur contiguously, or at a short distance, and may involve some mutations (such as substitutions, insertions, and deletions). Tandem repeats have been extensively studied also for their association with the class of repeat expansion diseases (mostly affecting the nervous system). Comparative studies on the output of different tools for finding tandem repeats highlighted significant differences among the sets of detected tandem repeats, while many authors pointed up how critical it is the right choice of parameters.
In this paper we present
By using the tool
We strongly believe that biologists can be interested in a tool that, not only gives them the possibility of using multiple search algorithm at the same time, with the same effort exerted in using just one of the systems, but also simplifies the burden of comparing and merging the results, thus expanding our capabilities in detecting important phenomena related to tandem repeats.
Url:
DOI: 10.1186/1471-2105-13-S4-S3
PubMed: 22536970
PubMed Central: 3303744
Affiliations:
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PMC:3303744Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases</title><author><name sortKey="Pellegrini, Marco" sort="Pellegrini, Marco" uniqKey="Pellegrini M" first="Marco" last="Pellegrini">Marco Pellegrini</name><affiliation wicri:level="1"><nlm:aff id="I1">Istituto di Informatica e Telematica, Consiglio Nazionale delle Ricerche, Pisa I-56124, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto di Informatica e Telematica, Consiglio Nazionale delle Ricerche, Pisa I-56124</wicri:regionArea><placeName><settlement type="city">Pise</settlement><region nuts="2">Toscane</region></placeName></affiliation></author><author><name sortKey="Renda, Maria Elena" sort="Renda, Maria Elena" uniqKey="Renda M" first="Maria Elena" last="Renda">Maria Elena Renda</name><affiliation wicri:level="1"><nlm:aff id="I1">Istituto di Informatica e Telematica, Consiglio Nazionale delle Ricerche, Pisa I-56124, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto di Informatica e Telematica, Consiglio Nazionale delle Ricerche, Pisa I-56124</wicri:regionArea><placeName><settlement type="city">Pise</settlement><region nuts="2">Toscane</region></placeName></affiliation></author><author><name sortKey="Vecchio, Alessio" sort="Vecchio, Alessio" uniqKey="Vecchio A" first="Alessio" last="Vecchio">Alessio Vecchio</name><affiliation wicri:level="4"><nlm:aff id="I2">Dipartimento di Ingegneria dell'Informazione, Università di Pisa, Pisa I-56122, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Ingegneria dell'Informazione, Università di Pisa, Pisa I-56122</wicri:regionArea><placeName><settlement type="city">Pise</settlement><region nuts="2">Toscane</region></placeName><orgName type="university">Université de Pise</orgName><placeName><settlement type="city">Pise</settlement><region type="region" nuts="2">Toscane</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22536970</idno><idno type="pmc">3303744</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303744</idno><idno type="RBID">PMC:3303744</idno><idno type="doi">10.1186/1471-2105-13-S4-S3</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000419</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000419</idno><idno type="wicri:Area/Pmc/Curation">000419</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000419</idno><idno type="wicri:Area/Pmc/Checkpoint">000281</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000281</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases</title><author><name sortKey="Pellegrini, Marco" sort="Pellegrini, Marco" uniqKey="Pellegrini M" first="Marco" last="Pellegrini">Marco Pellegrini</name><affiliation wicri:level="1"><nlm:aff id="I1">Istituto di Informatica e Telematica, Consiglio Nazionale delle Ricerche, Pisa I-56124, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto di Informatica e Telematica, Consiglio Nazionale delle Ricerche, Pisa I-56124</wicri:regionArea><placeName><settlement type="city">Pise</settlement><region nuts="2">Toscane</region></placeName></affiliation></author><author><name sortKey="Renda, Maria Elena" sort="Renda, Maria Elena" uniqKey="Renda M" first="Maria Elena" last="Renda">Maria Elena Renda</name><affiliation wicri:level="1"><nlm:aff id="I1">Istituto di Informatica e Telematica, Consiglio Nazionale delle Ricerche, Pisa I-56124, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto di Informatica e Telematica, Consiglio Nazionale delle Ricerche, Pisa I-56124</wicri:regionArea><placeName><settlement type="city">Pise</settlement><region nuts="2">Toscane</region></placeName></affiliation></author><author><name sortKey="Vecchio, Alessio" sort="Vecchio, Alessio" uniqKey="Vecchio A" first="Alessio" last="Vecchio">Alessio Vecchio</name><affiliation wicri:level="4"><nlm:aff id="I2">Dipartimento di Ingegneria dell'Informazione, Università di Pisa, Pisa I-56122, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Ingegneria dell'Informazione, Università di Pisa, Pisa I-56122</wicri:regionArea><placeName><settlement type="city">Pise</settlement><region nuts="2">Toscane</region></placeName><orgName type="university">Université de Pise</orgName><placeName><settlement type="city">Pise</settlement><region type="region" nuts="2">Toscane</region></placeName></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Tandem repeats are multiple duplications of substrings in the DNA that occur contiguously, or at a short distance, and may involve some mutations (such as substitutions, insertions, and deletions). Tandem repeats have been extensively studied also for their association with the class of repeat expansion diseases (mostly affecting the nervous system). Comparative studies on the output of different tools for finding tandem repeats highlighted significant differences among the sets of detected tandem repeats, while many authors pointed up how critical it is the right choice of parameters.</p></sec><sec><title>Results</title><p>In this paper we present <italic>TReaDS - Tandem Repeats Discovery Service</italic>, a <italic>tandem repeat meta search engine</italic>. <italic>TReaDS </italic>forwards user requests to several state of the art tools for finding tandem repeats and merges their outcome into a single report, providing a global, synthetic, and comparative view of the results. In particular, <italic>TReaDS </italic>allows the user to (<italic>i</italic>) simultaneously run different algorithms on the same data set, (<italic>ii</italic>) choose for each algorithm a different setting of parameters, and (<italic>iii</italic>) obtain a report that can be downloaded for further, off-line, investigations. We used <italic>TReaDS </italic>to investigate sequences associated with repeat expansion diseases.</p></sec><sec><title>Conclusions</title><p>By using the tool <italic>TReaDS </italic>we discover that, for 27 repeat expansion diseases out of a currently known set of 29, <italic>long fuzzy tandem repeats </italic>are covering the expansion loci. Tests with control sets confirm the specificity of this association. This finding suggests that long fuzzy tandem repeats can be a new class of cis-acting elements involved in the mechanisms leading to the expansion instability.</p><p>We strongly believe that biologists can be interested in a tool that, not only gives them the possibility of using multiple search algorithm at the same time, with the same effort exerted in using just one of the systems, but also simplifies the burden of comparing and merging the results, thus expanding our capabilities in detecting important phenomena related to tandem repeats.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Cummings, Cj" uniqKey="Cummings C">CJ Cummings</name></author><author><name sortKey="Zoghbi, Hy" uniqKey="Zoghbi H">HY Zoghbi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Usdin, K" uniqKey="Usdin K">K Usdin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mirkin, Sm" 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<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Bioinformatics</journal-id><journal-id journal-id-type="iso-abbrev">BMC Bioinformatics</journal-id><journal-title-group><journal-title>BMC Bioinformatics</journal-title></journal-title-group><issn pub-type="epub">1471-2105</issn><publisher><publisher-name>BioMed Central</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22536970</article-id><article-id pub-id-type="pmc">3303744</article-id><article-id pub-id-type="publisher-id">1471-2105-13-S4-S3</article-id><article-id pub-id-type="doi">10.1186/1471-2105-13-S4-S3</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research</subject></subj-group></article-categories><title-group><article-title>Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases</article-title></title-group><contrib-group><contrib contrib-type="author" id="A1"><name><surname>Pellegrini</surname><given-names>Marco</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>marco.pellegrini@iit.cnr.it</email></contrib><contrib contrib-type="author" corresp="yes" id="A2"><name><surname>Renda</surname><given-names>Maria Elena</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>elena.renda@iit.cnr.it</email></contrib><contrib contrib-type="author" id="A3"><name><surname>Vecchio</surname><given-names>Alessio</given-names></name><xref ref-type="aff" rid="I2">2</xref><email>a.vecchio@iet.unipi.it</email></contrib></contrib-group><aff id="I1"><label>1</label>Istituto di Informatica e Telematica, Consiglio Nazionale delle Ricerche, Pisa I-56124, Italy</aff><aff id="I2"><label>2</label>Dipartimento di Ingegneria dell'Informazione, Università di Pisa, Pisa I-56122, Italy</aff><pub-date pub-type="collection"><year>2012</year></pub-date><pub-date pub-type="epub"><day>28</day><month>3</month><year>2012</year></pub-date><volume>13</volume><issue>Suppl 4</issue><supplement><named-content content-type="supplement-title">Italian Society of Bioinformatics (BITS): Annual Meeting 2011</named-content><named-content content-type="supplement-editor">Paolo Romano and Manuela Helmer-Citterich</named-content></supplement><fpage>S3</fpage><lpage>S3</lpage><permissions><copyright-statement>Copyright ©2012 Pellegrini et al.; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2012</copyright-year><copyright-holder>Pellegrini et al.; licensee BioMed Central Ltd.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an open access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri xlink:href="http://www.biomedcentral.com/bmcbioinformatics/supplements/13/S4/S3"></self-uri><abstract><sec><title>Background</title><p>Tandem repeats are multiple duplications of substrings in the DNA that occur contiguously, or at a short distance, and may involve some mutations (such as substitutions, insertions, and deletions). Tandem repeats have been extensively studied also for their association with the class of repeat expansion diseases (mostly affecting the nervous system). Comparative studies on the output of different tools for finding tandem repeats highlighted significant differences among the sets of detected tandem repeats, while many authors pointed up how critical it is the right choice of parameters.</p></sec><sec><title>Results</title><p>In this paper we present <italic>TReaDS - Tandem Repeats Discovery Service</italic>, a <italic>tandem repeat meta search engine</italic>. <italic>TReaDS </italic>forwards user requests to several state of the art tools for finding tandem repeats and merges their outcome into a single report, providing a global, synthetic, and comparative view of the results. In particular, <italic>TReaDS </italic>allows the user to (<italic>i</italic>) simultaneously run different algorithms on the same data set, (<italic>ii</italic>) choose for each algorithm a different setting of parameters, and (<italic>iii</italic>) obtain a report that can be downloaded for further, off-line, investigations. We used <italic>TReaDS </italic>to investigate sequences associated with repeat expansion diseases.</p></sec><sec><title>Conclusions</title><p>By using the tool <italic>TReaDS </italic>we discover that, for 27 repeat expansion diseases out of a currently known set of 29, <italic>long fuzzy tandem repeats </italic>are covering the expansion loci. Tests with control sets confirm the specificity of this association. This finding suggests that long fuzzy tandem repeats can be a new class of cis-acting elements involved in the mechanisms leading to the expansion instability.</p><p>We strongly believe that biologists can be interested in a tool that, not only gives them the possibility of using multiple search algorithm at the same time, with the same effort exerted in using just one of the systems, but also simplifies the burden of comparing and merging the results, thus expanding our capabilities in detecting important phenomena related to tandem repeats.</p></sec></abstract><conference><conf-date>20-22 June 2011</conf-date><conf-name>Eighth Annual Meeting of the Italian Society of Bioinformatics (BITS)</conf-name><conf-loc>Pisa, Italy</conf-loc></conference></article-meta></front></pmc><affiliations><list><country><li>Italie</li></country><region><li>Toscane</li></region><settlement><li>Pise</li></settlement><orgName><li>Université de Pise</li></orgName></list><tree><country name="Italie"><region name="Toscane"><name sortKey="Pellegrini, Marco" sort="Pellegrini, Marco" uniqKey="Pellegrini M" first="Marco" last="Pellegrini">Marco Pellegrini</name></region><name sortKey="Renda, Maria Elena" sort="Renda, Maria Elena" uniqKey="Renda M" first="Maria Elena" last="Renda">Maria Elena Renda</name><name sortKey="Vecchio, Alessio" sort="Vecchio, Alessio" uniqKey="Vecchio A" first="Alessio" last="Vecchio">Alessio Vecchio</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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