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Bioinformatics Advance Access published online on November 29, 2005
Bioinformatics, 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
Received August 12, 2005
Revised November 10, 2005
Accepted November 24, 2005

Applications note

Identification of plant microRNA homologs

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

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

* To whom correspondence should be addressed.
Tobias Dezulian, E-mail: dezulian{at}informatik.uni-tuebingen.de


  Abstract

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


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