miRBase: Griffiths‐Jones, Sam. "The microRNA registry." Nucleic acids research 32.suppl 1 (2004): D109-D111.
Pre-miRNA prediction tools: Comparative genomics and homology-based approaches
Rfam: Gardner, Paul P., et al. "Rfam: Wikipedia, clans and the “decimal” release." Nucleic acids research 39.suppl 1 (2011): D141-D145.
MiRFinder: Huang, Ting-Hua, et al. "MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans." BMC bioinformatics 8.1 (2007): 341.
miRRim: Terai, Goro, et al. "miRRim: a novel system to find conserved miRNAs with high sensitivity and specificity." Rna 13.12 (2007): 2081-2090.
RNAmicro: Hertel, Jana, and Peter F. Stadler. "Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data." Bioinformatics 22.14 (2006): e197-e202.
BayesMiRNAfind: Yousef, Malik, et al. "Combining multi-species genomic data for microRNA identification using a Naive Bayes classifier." Bioinformatics 22.11 (2006): 1325-1334.
miRAlign: Wang, Xiaowo, et al. "MicroRNA identification based on sequence and structure alignment." Bioinformatics 21.18 (2005): 3610-3614.
ERPIN: Legendre, Matthieu, André Lambert, and Daniel Gautheret. "Profile-based detection of microRNA precursors in animal genomes." Bioinformatics 21.7 (2005): 841-845.
miRseeker: Lai, Eric C., et al. "Computational identification of Drosophila microRNA genes." Genome Biol 4.7 (2003): R42.
Ab initio methods
miRNAFold: Tempel, Sébastien, and Fariza Tahi. "A fast ab-initio method for predicting miRNA precursors in genomes." Nucleic acids research 40.11 (2012): e80-e80.
miRPara: Wu, Yonggan, et al. "MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences." BMC bioinformatics 12.1 (2011): 107.
MIReNA: Mathelier, Anthony, and Alessandra Carbone. "MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data." Bioinformatics 26.18 (2010): 2226-2234.
SSCprofiler: Oulas, Anastasis, et al. "Prediction of novel microRNA genes in cancer-associated genomic regions—a combined computational and experimental approach." Nucleic acids research 37.10 (2009): 3276-3287.
microPred: Batuwita, Rukshan, and Vasile Palade. "microPred: effective classification of pre-miRNAs for human miRNA gene prediction." Bioinformatics 25.8 (2009): 989-995.
Virgo:Kumar, Shiva, Faraz A. Ansari, and Vinod Scaria. "Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features." Virology journal 6.1 (2009): 129.
miRANK: Xu, Yunpen, Xuefeng Zhou, and Weixiong Zhang. "MicroRNA prediction with a novel ranking algorithm based on random walks." Bioinformatics 24.13 (2008): i50-i58.
CID-miRNA: Tyagi, Sonika, et al. "CID-miRNA: A web server for prediction of novel miRNA precursors in human genome." Biochemical and biophysical research communications 372.4 (2008): 831-834.
mir-KDE: Chang, Darby TH, Chih-Ching Wang, and Jian-Wei Chen. "Using a kernel density estimation based classifier to predict species-specific microRNA precursors." BMC bioinformatics 9.Suppl 12 (2008): S2.
miPred: Jiang, Peng, et al. "MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features." Nucleic acids research 35.suppl 2 (2007): W339-W344.
miRPred: Brameier, Markus, and Carsten Wiuf. "Ab initio identification of human microRNAs based on structure motifs." BMC bioinformatics 8.1 (2007): 478.
VMir: Grundhoff, Adam, Christopher S. Sullivan, and Don Ganem. "A combined computational and microarray-based approach identifies novel microRNAs encoded by human gamma-herpesviruses." Rna 12.5 (2006): 733-750.
Triplet-SVM: Xue, Chenghai, et al. "Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine." BMC bioinformatics 6.1 (2005): 310.
miR-abela: Sewer, Alain, et al. "Identification of clustered microRNAs using an ab initio prediction method." BMC bioinformatics 6.1 (2005): 267.
ProMiR I/II: Nam, Jin-Wu, et al. "Human microRNA prediction through a probabilistic co-learning model of sequence and structure." Nucleic acids research 33.11 (2005): 3570-3581.
MiRscan: Lim, Lee P., et al. "The microRNAs of Caenorhabditis elegans." Genes & development 17.8 (2003): 991-1008.
MiRNA prediction tools:
miRdup: Leclercq, Mickael, Abdoulaye Banire Diallo, and Mathieu Blanchette. "Computational prediction of the localization of microRNAs within their pre-miRNA." Nucleic acids research (2013).
miRRim2: Terai, Goro, et al. "Prediction of Conserved Precursors of miRNAs and Their Mature Forms by Integrating Position-Specific Structural Features." PloS one 7.9 (2012): e44314.
MiRmat: He, Chenfeng, et al. "MiRmat: mature microRNA sequence prediction." PloS one 7.12 (2012): e51673.
FoMmir: Shen, Wei, et al. "MicroRNA Prediction Using a Fixed-Order Markov Model Based on the Secondary Structure Pattern." PloS one 7.10 (2012): e48236.
MaturePred: Xuan, Ping, et al. "MaturePred: efficient identification of microRNAs within novel plant pre-miRNAs." PLoS one 6.11 (2011): e27422.
MiRPara: Wu, Yonggan, et al. "MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences." BMC bioinformatics 12.1 (2011): 107.
MatureBayes: Gkirtzou, Katerina, et al. "MatureBayes: a probabilistic algorithm for identifying the mature miRNA within novel precursors." PloS one 5.8 (2010): e11843.
mirCos: Sheng, Ying, Pär G. Engström, and Boris Lenhard. "Mammalian microRNA prediction through a support vector machine model of sequence and structure." PloS one 2.9 (2007): e946.
BayesMiRNAfind: Yousef, Malik, et al. "Combining multi-species genomic data for microRNA identification using a Naive Bayes classifier." Bioinformatics 22.11 (2006): 1325-1334.
ProMiR I/II: Nam, Jin-Wu, et al. "Human microRNA prediction through a probabilistic co-learning model of sequence and structure." Nucleic acids research 33.11 (2005): 3570-3581.
MiRalign: Wang, Xiaowo, et al. "MicroRNA identification based on sequence and structure alignment." Bioinformatics 21.18 (2005): 3610-3614.
MIRcheck: Jones-Rhoades, Matthew W., and David P. Bartel. "Computational identification of plant microRNAs and their targets, including a stress-induced miRNA." Molecular cell 14.6 (2004): 787-799.