TelematiV1, PubMed, Curation, bibRecord, 000291

Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases.

Identifieur interne : 000291 ( PubMed/Curation ); précédent : 000290; suivant : 000292

Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases.

Auteurs : Marco Pellegrini [Italie] ; Maria Elena Renda ; Alessio Vecchio

Source :

BMC bioinformatics [ 1471-2105 ] ; 2012.

RBID : pubmed:22536970

Descripteurs français

English descriptors

KwdEn :
- Algorithms, DNA Repeat Expansion, Humans, Neurodegenerative Diseases (genetics), Neuromuscular Diseases (genetics), Peptides (genetics), Polymorphism, Single Nucleotide, Search Engine, Sequence Analysis, DNA (methods).
MESH :
- chemical , genetics : Peptides.
- genetics : Neurodegenerative Diseases, Neuromuscular Diseases.
- methods : Sequence Analysis, DNA.
- Algorithms, DNA Repeat Expansion, Humans, Polymorphism, Single Nucleotide, Search Engine.

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.

DOI: 10.1186/1471-2105-13-S4-S3
PubMed: 22536970

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Le document en format XML

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<author><name sortKey="Pellegrini, Marco" sort="Pellegrini, Marco" uniqKey="Pellegrini M" first="Marco" last="Pellegrini">Marco Pellegrini</name>
<affiliation wicri:level="1"><nlm:affiliation>Istituto di Informatica e Telematica, Consiglio Nazionale delle Ricerche, Pisa I-56124, Italy.</nlm:affiliation>
<country xml:lang="fr">Italie</country>
<wicri:regionArea>Istituto di Informatica e Telematica, Consiglio Nazionale delle Ricerche, Pisa I-56124</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Renda, Maria Elena" sort="Renda, Maria Elena" uniqKey="Renda M" first="Maria Elena" last="Renda">Maria Elena Renda</name>
</author>
<author><name sortKey="Vecchio, Alessio" sort="Vecchio, Alessio" uniqKey="Vecchio A" first="Alessio" last="Vecchio">Alessio Vecchio</name>
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<series><title level="j">BMC bioinformatics</title>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term>
<term>DNA Repeat Expansion</term>
<term>Humans</term>
<term>Neurodegenerative Diseases (genetics)</term>
<term>Neuromuscular Diseases (genetics)</term>
<term>Peptides (genetics)</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Search Engine</term>
<term>Sequence Analysis, DNA (methods)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term>
<term>Analyse de séquence d'ADN ()</term>
<term>Expansion de séquence répétée de l'ADN</term>
<term>Humains</term>
<term>Maladies neurodégénératives (génétique)</term>
<term>Maladies neuromusculaires (génétique)</term>
<term>Moteur de recherche</term>
<term>Peptides (génétique)</term>
<term>Polymorphisme de nucléotide simple</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Peptides</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Neurodegenerative Diseases</term>
<term>Neuromuscular Diseases</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Maladies neurodégénératives</term>
<term>Maladies neuromusculaires</term>
<term>Peptides</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>DNA Repeat Expansion</term>
<term>Humans</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Search Engine</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term>
<term>Analyse de séquence d'ADN</term>
<term>Expansion de séquence répétée de l'ADN</term>
<term>Humains</term>
<term>Moteur de recherche</term>
<term>Polymorphisme de nucléotide simple</term>
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<front><div type="abstract" xml:lang="en">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.</div>
</front>
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<pubmed><MedlineCitation Owner="NLM" Status="MEDLINE"><PMID Version="1">22536970</PMID>
<DateCreated><Year>2012</Year>
<Month>04</Month>
<Day>27</Day>
</DateCreated>
<DateCompleted><Year>2012</Year>
<Month>11</Month>
<Day>06</Day>
</DateCompleted>
<DateRevised><Year>2015</Year>
<Month>02</Month>
<Day>25</Day>
</DateRevised>
<Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2105</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>13 Suppl 4</Volume>
<PubDate><Year>2012</Year>
</PubDate>
</JournalIssue>
<Title>BMC bioinformatics</Title>
<ISOAbbreviation>BMC Bioinformatics</ISOAbbreviation>
</Journal>
<ArticleTitle>Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases.</ArticleTitle>
<Pagination><MedlinePgn>S3</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2105-13-S4-S3</ELocationID>
<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">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.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">In this paper we present TReaDS - Tandem Repeats Discovery Service, a tandem repeat meta search engine. TReaDS 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, TReaDS allows the user to (i) simultaneously run different algorithms on the same data set, (ii) choose for each algorithm a different setting of parameters, and (iii) obtain a report that can be downloaded for further, off-line, investigations. We used TReaDS to investigate sequences associated with repeat expansion diseases.</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">By using the tool TReaDS we discover that, for 27 repeat expansion diseases out of a currently known set of 29, long fuzzy tandem repeats 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.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.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Pellegrini</LastName>
<ForeName>Marco</ForeName>
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<AffiliationInfo><Affiliation>Istituto di Informatica e Telematica, Consiglio Nazionale delle Ricerche, Pisa I-56124, Italy.</Affiliation>
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<Author ValidYN="Y"><LastName>Renda</LastName>
<ForeName>Maria Elena</ForeName>
<Initials>ME</Initials>
</Author>
<Author ValidYN="Y"><LastName>Vecchio</LastName>
<ForeName>Alessio</ForeName>
<Initials>A</Initials>
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<Language>eng</Language>
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<MeshHeadingList><MeshHeading><DescriptorName MajorTopicYN="Y" UI="D000465">Algorithms</DescriptorName>
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<MeshHeading><DescriptorName MajorTopicYN="N" UI="D020641">Polymorphism, Single Nucleotide</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName MajorTopicYN="Y" UI="D057386">Search Engine</DescriptorName>
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<QualifierName MajorTopicYN="Y" UI="Q000379">methods</QualifierName>
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Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases.

Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases.

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