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A comparative account of microRNA resources, feature-validations and application-based categorizations : SPECIES: fly
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
miRBase
http://www.mirbase.org/
A major microRNA repository comprising of microRNA sequences and annotation obtained from published literature wherein both precursor and mature sequences can be retrieved from the database.
Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011 Jan;39(Database issue):D152-7. Epub 2010 Oct 30. PubMed PMID: 21037258 Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8. Epub 2007 Nov 8. PubMed PMID: 17991681
2011
66
Diana micro T
1. http://www.microrna.gr/microT 2. http:www.microrna.gr/microT-v4
Computational analysis of microRNA targets by using conserved and non-conserved microRNA recognition elements to derive the prediction score.
1. Maragkakis M, Vergoulis T, Alexiou P, Reczko M, Plomaritou Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG. DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W273-6. Epub 2009 Apr 30. PubMed PMID: 19406924K,
2009
100
EIMMO
1.http://piech.kaist.ac.kr/dynamod 2. http://biocondor6.kaist.ac.kr/dynamod/
Tool for microRNA target prediction and enrichment and depletion analysis in Gene Ontology terms.
Gaidatzis D, van Nimwegen E, Gaidatzis D, van Nimwegen E, Hausser J, Zavolan M. Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics. 2007 Mar 1;8:69. Erratum in: BMC Bioinformatics. 2007 Jul 12;8(1):248. PubMed PMID: 17331257
2007
100
miRNEST
http://mirnest.amu.edu.pl
Comprehensive database on animal, plant and virus microRNA including details on species that are of importance in medical and agricultural research.
Szczesniak MW, Deorowicz S, Gapski J, Kaczynski L, Makalowska I. miRNEST database: an integrative approach in microRNA search and annotation. Nucleic Acids Res. 2012 Jan;40(Database issue):D198-204. Epub 2011 Dec 1. PubMed PMID: 22135287; PubMed Central PMCID: PMC3245016.
2012
100
MovingTargets
URL not found
In silico tool for prediction of microRNA targets in Drosophila by the process of targeting a specific gene or by conducting a genome-wide search.
Burgler C, Macdonald PM. Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method. BMC Genomics. 2005 Jun 8;6:88. PubMed PMID: 15943864; PubMed Central PMCID: PMC1180435.
2005
100
The MovingTargets software is available on DVD by request
RBPDB- RNA-Binding Protein DataBase
http://rbpdb.ccbr.utoronto.ca/
The RNA-Binding Protein DataBase (RBPDB) predominantly contains experimentally derived information on RNA-binding sites, obtained by manual curation from primary literature sources.
Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR. RBPDB: a database of RNA-binding specificities. Nucleic Acids Res. 2011 Jan;39(Database issue):D301-8. Epub 2010 Oct 29. PubMed PMID: 21036867
2010
100
RBPmap
http://rbpmap.technion.ac.il/
RBPmap enables the users to select motifs from a large database of experimentally defined motifs. RBPmap incorporates a position-specific background model, designed uniquely for different genomic regions, such as splice sites, 5’ and 3’ UTRs, non-coding RNA and intergenic regions.
Inbal Paz, 1 Idit Kosti, 1 Manuel Ares, Jr, 2 Melissa Cline, 3 and Yael Mandel-Gutfreund.RBPmap: A web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Res. 2014 Jul 1; 42(Web Server issue): W361–W367. PMCID: PMC4086114
2014
100
smiRNAdb
http://www.mirz.unibas.ch/cloningprofiles/
Online resource for expression information on small RNAs (mostly miRNAs) for human, mouse, rat, zebrafish, worm and fruitfly.
Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foà R, Schliwka J, Fuchs U, Novosel A, Müller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell. 2007 Jun 29;129(7):1401-14. PubMed PMID: 17604727; PubMed Central PMCID: PMC2681231.
2007
100
Datasets downloadable
 
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