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miROrtho: computational survey of microRNA genes.

Abstract：

:MicroRNAs (miRNAs) are short, non-protein coding RNAs that direct the widespread phenomenon of post-transcriptional regulation of metazoan genes. The mature approximately 22-nt long RNA molecules are processed from genome-encoded stem-loop structured precursor genes. Hundreds of such genes have been experimentally validated in vertebrate genomes, yet their discovery remains challenging, and substantially higher numbers have been estimated. The miROrtho database (http://cegg.unige.ch/mirortho) presents the results of a comprehensive computational survey of miRNA gene candidates across the majority of sequenced metazoan genomes. We designed and applied a three-tier analysis pipeline: (i) an SVM-based ab initio screen for potent hairpins, plus homologs of known miRNAs, (ii) an orthology delineation procedure and (iii) an SVM-based classifier of the ortholog multiple sequence alignments. The web interface provides direct access to putative miRNA annotations, ortholog multiple alignments, RNA secondary structure conservation, and sequence data. The miROrtho data are conceptually complementary to the miRBase catalog of experimentally verified miRNA sequences, providing a consistent comparative genomics perspective as well as identifying many novel miRNA genes with strong evolutionary support.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Gerlach D,Kriventseva EV,Rahman N,Vejnar CE,Zdobnov EM

doi

10.1093/nar/gkn707

subject

Has Abstract

pub_date

2009-01-01 00:00:00

pages

D111-7

issue

Database issue

eissn

0305-1048

issn

1362-4962

pii

gkn707

journal_volume

37

pub_type

杂志文章

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