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Bioinformatics Advance Access originally published online on November 29, 2005
Bioinformatics 2006 22(3):359-360; doi:10.1093/bioinformatics/bti802
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Identification of plant microRNA homologs

Tobias Dezulian 1,*, Michael Remmert 1, Javier F. Palatnik 2, Detlef Weigel 2 and Daniel H. Huson 1

1Center for Bioinformatics Tübingen, Tübingen University Germany
2Max Planck Institute for Developmental Biology, Tübingen Germany

*To whom correspondence should be addressed.

Summary: MicroRNAs (miRNAs) are a recently discovered class of non-coding RNAs that regulate gene and protein expression in plants and animals. MiRNAs have so far been identified mostly by specific cloning of small RNA molecules, complemented by computational methods. We present a computational identification approach that is able to identify candidate miRNA homologs in any set of sequences, given a query miRNA. The approach is based on a sequence similarity search step followed by a set of structural filters.

Availability: microHARVESTER is offered as a web-service and additionally as source code upon request at http://www-ab.informatik.uni-tuebingen.de/software/microHARVESTER

Contact: dezulian{at}informatik.uni-tuebingen.de

Received on August 12, 2005; revised on November 10, 2005; accepted on November 24, 2005

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