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An approach to identify over-represented cis-elements in related sequences

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Journal
Nucleic Acids Research
0305-1048
Publisher
Oxford University Press
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Abstract

gkq1027 152..157 miRBase: integrating microRNA annotation and deep-sequencing data Ana Kozomara and Sam Griffiths-Jones* Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK Received September 15, 2010; Accepted October 10, 2010 ABSTRACT miRBase is the primary online repository for all microRNA sequences and annotation. The current release (miRBase 16) contains over 15 000 microRNA gene loci in over 140 species, and over 17 000 distinct mature microRNA sequences. Deep- sequencing technologies have delivered a sharp rise in the rate of novel microRNA discovery. We have mapped reads from short RNA deep-sequencing ex- periments to microRNAs in miRBase and developed web interfaces to view these mappings. The user can view all read data associated with a given microRNA annotation, filter reads by experiment and count, and search for microRNAs by tissue- and stage-specific expression. These data can be used as a proxy for relative expression levels of microRNA sequences, provide detailed evidence for microRNA annotations and alternative isoforms of mature microRNAs, and allow us to revisit previous annotations. miRBase is available online at: http://www.mirbase.org/. INTRODUCTION miRBase is the primary online repository for microRNA sequences and annotations. The main aims of miRBase are: (1) to curate a consistent nomenclature scheme by which novel microRNAs are named; (2) to act as the central repository for all published microRNA sequences, and to facilitate online searching and bulk download of all microRNA data; (3) to provide human-readable and computer-parsable annotation of microRNA sequences (for example, functional data, references, genome mappings); (4) to provide access to the primary evidence that supports microRNA annotations; and (5) to link to and aggregate microRNA target predic- tions and validations. The miRBase database was established in 2002 (then called the microRNA Registry) to provide microRNA

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