- MicroInspector (2005): a web tool for detection of miRNA binding sites in an RNA sequence.
- MiPred (2007): a tool as a classification of real and pseudo microRNA precursors using random forest prediction model with combined features.
- miR2Disease (2009): a database which provides a comprehensive resource of microRNA deregulation in various human diseases.
- miRBase (2008): a searchable database of published miRNA sequences and annotation.
- miRGator (2010): an integrated system for functional investigation of microRNAs.
- miRGen (2007): a database for the study of animal microRNA genomic organization and function.
- miRNAminer (2008): a web-based tool used for homologous miRNA gene search in several species.
- miROrtho (2009): a database presents the results of a comprehensive computational survey of miRNA gene candidates across the majority of sequenced metazoan genomes.
- MMIA (2009): a web tool for examining biological functions of microRNA expression.
- Rfam (2009): a resource for predicted microRNA targets and expression.
- TransmiR (2010): a database provides transcription factor-microRNA regulations, miRNA function annotation and miRNA-associated disease annotation.
miRNA Target Prediction
- DIANA-microT (2009): a database elucidating microRNA functions through target prediction.
- MicroRNA.org (2008): a microRNA target prediction and functional annotation database with a wiki interface.
- miRDB (2008): a comprehensive resource of microRNA target predictions and expression profiles.
- miRecords (2009): an integrated resource for microRNA-target interactions.
- NBmiRTar (2007): a web tool provides a machine learning for microRNA targets.
- PicTar (2005): an algorithm for the identification of microRNA targets.
- RNAhybrid (2009): a tool , primarily meant as a means for microRNA target prediction, for finding the minimum free energy hybridisation of a long and a short RNA.
- TargetScan (2009): Prediction of microRNA targets.
miRNA and Target Interaction
- miRNAMap (2006): a tool provides genomic maps of microRNA genes and their target genes in mammalian genomes.
- miRNApath (2007): an online database that uses miRNA target genes to link miRNAs to metabolic pathways.
- miRTarBase (2010): a database curates experimentally validated microRNA-target interactions.
- PMRD (2010): a plant microRNA database, involving miRNAs and their target genes, especially model plants and major crops.
Novel miRNA or Hairpin Prediction
- miRanalyzer (2009): a microRNA detection and analysis tool for next-generation sequencing experiments.
- mirTool (2010): a comprehensive web server provides detailed annotation information for known miRNAs, such as miRNA/miRNA*, predicts novel miRNAs that have not been characterized before and so on.
- RNA22 (2006): a tool which provides the functions of microRNA target detection & precursor prediction
- Vir-Mir db (2008): a database provides predicted viral miRNA hairpins based on taxonomic classification, and a host target gene prediction service based on the RNAhybrid program and the 3'-UTR gene sequences of human, mouse, rat, zebrafish, rice and Arabidopsis.
- GeneCards: a searchable, integrated database of human genes.
- GO: a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases.
- HGNC: HUGO Gene Nomenclature Committee.
- NCBI: the National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.
- OMIM: Online Mendelian Inheritance in Man.
- Pubmed: a service of the U.S. National Library of Medicine and the National Institutes of Health.
- RefSeq: NCBI Reference Sequence.