Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases
Identifieur interne : 000801 ( Ncbi/Checkpoint ); précédent : 000800; suivant : 000802Tandem 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.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- 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.
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
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<series><title level="j">BMC Bioinformatics</title>
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<term>DNA Repeat Expansion</term>
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<term>Neuromuscular Diseases (genetics)</term>
<term>Peptides (genetics)</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Search Engine</term>
<term>Sequence Analysis, DNA (methods)</term>
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<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>
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<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>
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<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Maladies neurodégénératives</term>
<term>Maladies neuromusculaires</term>
<term>Peptides</term>
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<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>
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<term>Analyse de séquence d'ADN</term>
<term>Expansion de séquence répétée de l'ADN</term>
<term>Humains</term>
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<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>
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</back>
</TEI>
<affiliations><list><country><li>Italie</li>
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<region><li>Toscane</li>
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<settlement><li>Pise</li>
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<orgName><li>Université de Pise</li>
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</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>
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<name sortKey="Vecchio, Alessio" sort="Vecchio, Alessio" uniqKey="Vecchio A" first="Alessio" last="Vecchio">Alessio Vecchio</name>
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