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PMID: 23716633 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

miRmap web: Comprehensive microRNA target prediction online.

Nucleic acids research ·Vol. 41 ·No. Web Server issue ·2013-07-00 ·Pages W165-8

Vejnar CE, Blum M, Zdobnov EM

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.

MeSH Terms
3' Untranslated Regions Gene Expression Regulation Internet MicroRNAs/chemistry,metabolism RNA, Messenger/chemistry,metabolism Sequence Analysis, RNA Software Thermodynamics
Chemicals
3' Untranslated Regions MicroRNAs RNA, Messenger
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Vejnar Charles E
Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.
Blum Matthias
Zdobnov Evgeny M
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17 references, click to expand
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkt430
Published
2013-07-00
Epub
2013-00-28
Pages
W165-8
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3692044
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkt430 PMC Full Text View journal details
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