miRBase: tools for microRNA genomics

miRBase: tools for microRNA genomics

2008 | Sam Griffiths-Jones¹,*, Harpreet Kaur Saini², Stijn van Dongen² and Anton J. Enright²
miRBase is the central online repository for microRNA (miRNA) nomenclature, sequence data, annotation, and target prediction. The current release (10.0) contains 5071 miRNA loci from 58 species, expressing 5922 distinct mature miRNA sequences, a growth of over 2000 sequences in the past 2 years. miRBase provides a range of data to facilitate studies of miRNA genomics, including genomic coordinates, miRNA clusters, overlap with annotated transcripts, and graphical views of genomic features in model organisms. It also allows prediction of the likely boundaries of many miRNA primary transcripts. miRBase has three main functions: (i) miRBase::Registry provides a confidential service for the independent assignment of names to novel miRNA genes prior to their publication. (ii) miRBase::Sequences provides miRNA sequence data, annotation, references, and links to other resources for all published miRNAs. (iii) miRBase::Targets provides an automated pipeline for the prediction of targets for all published animal miRNAs. The miRNA nomenclature scheme includes a three or four letter species prefix and a numeric suffix. miRBase provides information about gene and mature miRNA sequence families in dedicated fields. The published miRNA literature is extensive, and miRBase provides tools to distribute miRNA genomic information. miRBase provides genomic coordinates for all miRNAs, miRNA gene context, clustered miRNAs, and genomic features. It also provides tools to visualize the relative positions of these predictions and mappings with respect to annotated miRNA genes and clusters. miRBase is available at http://microrna.sanger.ac.uk/. All data are available for download from the FTP site.miRBase is the central online repository for microRNA (miRNA) nomenclature, sequence data, annotation, and target prediction. The current release (10.0) contains 5071 miRNA loci from 58 species, expressing 5922 distinct mature miRNA sequences, a growth of over 2000 sequences in the past 2 years. miRBase provides a range of data to facilitate studies of miRNA genomics, including genomic coordinates, miRNA clusters, overlap with annotated transcripts, and graphical views of genomic features in model organisms. It also allows prediction of the likely boundaries of many miRNA primary transcripts. miRBase has three main functions: (i) miRBase::Registry provides a confidential service for the independent assignment of names to novel miRNA genes prior to their publication. (ii) miRBase::Sequences provides miRNA sequence data, annotation, references, and links to other resources for all published miRNAs. (iii) miRBase::Targets provides an automated pipeline for the prediction of targets for all published animal miRNAs. The miRNA nomenclature scheme includes a three or four letter species prefix and a numeric suffix. miRBase provides information about gene and mature miRNA sequence families in dedicated fields. The published miRNA literature is extensive, and miRBase provides tools to distribute miRNA genomic information. miRBase provides genomic coordinates for all miRNAs, miRNA gene context, clustered miRNAs, and genomic features. It also provides tools to visualize the relative positions of these predictions and mappings with respect to annotated miRNA genes and clusters. miRBase is available at http://microrna.sanger.ac.uk/. All data are available for download from the FTP site.
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