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miRmap web: Comprehensive microRNA target prediction online

Blum, Matthias
Published in Nucleic Acids Research. 2013, vol. 41, no. Web Server issue, p. W165-8
Abstract MicroRNAs (miRNAs) posttranscriptionally repress the expression of protein-coding genes. Based on the partial complementarity between miRNA and messenger RNA pairs with a mandatory so-called 'seed' sequence, many thousands of potential targets can be identified. Our open-source software library, miRmap, ranks these potential targets with a biologically meaningful criterion, the repression strength. MiRmap combines thermodynamic, evolutionary, probabilistic and sequence-based features, which cover features from TargetScan, PITA, PACMIT and miRanda. Our miRmap web application offers a user-friendly and feature-rich resource for browsing precomputed miRNA target predictions for model organisms, as well as for predicting and ranking targets for user-submitted sequences. MiRmap web integrates sorting, filtering and exporting of results from multiple queries, as well as providing programmatic access, and is available at http://mirmap.ezlab.org.
Keywords 3' Untranslated RegionsGene Expression RegulationInternetMicroRNAs/chemistry/metabolismRNA, Messenger/chemistry/metabolismSequence Analysis, RNASoftwareThermodynamics
PMID: 23716633
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Research group Génomique Evolutionnaire Computationnelle (830)
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VEJNAR, Charles, BLUM, Matthias, ZDOBNOV, Evgeny. miRmap web: Comprehensive microRNA target prediction online. In: Nucleic Acids Research, 2013, vol. 41, n° Web Server issue, p. W165-8. https://archive-ouverte.unige.ch/unige:30574

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Deposited on : 2013-10-22

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