MicroRNA

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

TarBase
1. http://www.diana.pcbi.upenn.edu/tarbase 2. http://microrna.gr/tarbase

Manually curated database of experimentally supported microRNA (miRNA) targets in several animal SPECIES: plants and viruses.

Sethupathy P, Corda B, Hatzigeorgiou AG. TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA. 2006 Feb;12(2):192-7. Epub 2005 Dec 22. PubMed PMID: 16373484.

2005

The first URL is not working, as on 25 Feb 2017

psRNATarget
http://plantgrn.noble.org/psRNATarget/

Web based resource for plant small RNA target study and for use in high-throughput analysis of next generation sequencing data.

Dai X, Zhao PX. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W155-9. Epub 2011 May 27. PubMed PMID: 21622958; PubMed Central PMCID: PMC3125753.

2011

ASRP- Arabidopsis Small RNA Project Database
http://asrp.cgrb.oregonstate.edu

Serves as a repository for small RNA sequences cloned from several Arabidopsis genotypes and tissues.

Gustafson AM, Allen E, Givan S, Smith D, Carrington JC, Kasschau KD. ASRP: the Arabidopsis Small RNA Project Database. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D637-40. PubMed PMID: 15608278

2005

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Currently a major part of ASRP data is available at the Arabidopsis small RNA database maintained by Blake Meyers and Pamela Green
Currently a major part of ASRP data is available at the Arabidopsis small RNA database maintained by Blake Meyers and Pamela Green

CSRDB- Cereal Small RNA Database
http://sundarlab.ucdavis.edu/smrnas/

A bioinformatic resource for cereal crops, the Cereal Small RNA Database (CSRDB), consists of extensive data sets of maize and rice smRNA sequences obtained from high-throughput pyrosequencing.

Johnson C, Bowman L, Adai AT, Vance V, Sundaresan V. CSRDB: a small RNA integrated database and browser resource for cereals. Nucleic Acids Res. 2007 Jan;35(Database issue):D829-33. Epub 2006 Dec 14. PubMed PMID: 17169981; PubMed Central PMCID: PMC1781248.

2007

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findMiRNA
http://sundarlab.ucdavis.edu/mirna/

Bioinfomatic tool that uses single genome method to predict microRNAs in Arabidopsis thaliana.

Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, Sundaresan V. Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res. 2005 Jan;15(1):78-91. PubMed PMID: 15632092; PubMed Central PMCID: PMC540280.

2005

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Leaf senescence database
http://www.eplantsenescence.org/

Leaf senescence database (LSD) has information on 1145 senescence associated genes (SAGs) from 21 species including data on microRNA interactions.

Liu X, Li Z, Jiang Z, Zhao Y, Peng J, Jin J, Guo H, Luo J. LSD: a leaf senescence database. Nucleic Acids Res. 2011 Jan;39(Database issue):D1103-7. Epub 2010 Nov 18. PubMed PMID: 21097471

2011

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MaturePred
http://nclab.hit.edu.cn/maturepred/

Software application that predicts start sites of mature microRNA from newly identified precursor microRNA sequences in plants and animals.

Xuan P, Guo M, Huang Y, Li W, Huang Y. MaturePred: efficient identification of microRNAs within novel plant pre-miRNAs. PLoS One. 2011;6(11):e27422. Epub 2011 Nov 16. PubMed PMID: 22110646; PubMed Central PMCID: PMC3217989.

2011

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Dataset downloadable
Dataset downloadable

microHARVESTER
http://www-ab.informatik.uni-tuebingen.de/software/microHARVESTER

Tool designed to determine potential microRNA homologs in plants.

Dezulian T, Remmert M, Palatnik JF, Weigel D, Huson DH. Identification of plant microRNA homologs. Bioinformatics. 2006 Feb 1;22(3):359-60. Epub 2005 Nov 29. PubMed PMID: 16317073.

2006

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Downloadable on request. Service temporarily unavailable on 7-4-12, 22-4-12, 24-5-12, 29-6-12 , 18-7-12.
Downloadable on request. Service temporarily unavailable on 7-4-12, 22-4-12, 24-5-12, 29-6-12 , 18-7-12.

MicroPC
http://www.biotec.or.th/isl/micropc

An extensive resource which enables identifying potential microRNAs, target sites and their analysis in plants.

Mhuantong W, Wichadakul D. MicroPC (microPC): A comprehensive resource for predicting and comparing plant microRNAs. BMC Genomics. 2009 Aug 7;10:366. PubMed PMID: 19660144; PubMed Central PMCID: PMC2907689.

2009

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Dataset downloadable
Dataset downloadable

mirEX
1. http://comgen.pl/mirex/ 2. http://bioinfo.amu.edu.pl/mirex

A web interface for investigational studies and evaluation of plant pri-microRNA expression data (Arabidopsis pri-microRNA expression atlas) such as in unraveling the role of microRNAs that assist in guiding plant development, organogenesis and reaction to different stresses.

Bielewicz D, Dolata J, Zielezinski A, Alaba S, Szarzynska B, Szczesniak MW, Jarmolowski A, Szweykowska-Kulinska Z, Karlowski WM. mirEX: a platform for comparative exploration of plant pri-miRNA expression data. Nucleic Acids Res. 2011 Oct 19. [Epub ahead of print] PubMed PMID: 22013167.

2011

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miRNAXpress
URL not found

In silico tool designed to study the functional state of microRNAs in plants.

Zilberstein CB, Ziv-Ukelson M, Pinter RY, Yakhini Z. A high-throughput approach for associating MicroRNAs with their activity conditions. J Comput Biol. 2006 Mar;13(2):245-66. PubMed PMID: 16597238.

2006

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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

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miRTour
http://bio2server.bioinfo.uni-plovdiv.bg/miRTour/

Bioinformatics pipeline for identification of plant microRNA and target prediction

Milev I, Yahubyan G, Minkov I, Baev V. miRTour: Plant miRNA and target prediction tool. Bioinformation. 2011;6(6):248-9. Epub 2011 Jun 6. PubMed PMID: 21887016

2011

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miRu
1. http://plantgrn.noble.org/psRNATarget/ 2. http://bioinfo3.noble.org/miRU.htm

Computational tool for prediction of plant microRNA target genes.

Zhang Y. miRU: an automated plant miRNA target prediction server. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W701-4. PubMed PMID: 15980567; PubMed Central PMCID: PMC1160144.

2005

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Redirected to psRNATarget site
Redirected to psRNATarget site

miSolRNA
http://www.misolrna.org/

Database on tomato microRNAs, their predicted targets and expression.

Bazzini AA, As\EDs R, Gonz\E1lez V, Bassi S, Conte M, Soria M, Fernie AR, Asurmendi S, Carrari F. miSolRNA: A tomato micro RNA relational database. BMC Plant Biol. 2010 Nov 8;10:240. PubMed PMID: 21059227; PubMed Central PMCID: PMC3095322.

2010

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The data and source code is available for download at http://fix.misolrna.org/miRNA.tar.gz. The software license is General Public License version 3.
The data and source code is available for download at http://fix.misolrna.org/miRNA.tar.gz. The software license is General Public License version 3.

NovoMIR
http://www.biophys.uni-duesseldorf.de/

In silico tool for prediction of microRNA coding regions in a single plant genome in the absence of details on microRNA target or comparative genomics.

Teune JH, Steger G. NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome. J Nucleic Acids. 2010 Sep 13;2010. pii: 495904. PubMed PMID: 20871826; PubMed Central PMCID: PMC2943127.

2010

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To be validated
To be validated

PlantMiRNAPred
http://nclab.hit.edu.cn/PlantMiRNAPred/

Tool for plant precursor microRNA classification as true or pseudo candidates.

Xuan P, Guo M, Liu X, Huang Y, Li W, Huang Y. PlantMiRNAPred: efficient classification of real and pseudo plant pre-miRNAs. Bioinformatics. 2011 May 15;27(10):1368-76. Epub 2011 Mar 26. PubMed PMID: 21441575.

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The web service of PlantMiRNAPred, the training datasets, the testing datasets and the selected features are freely available.
The web service of PlantMiRNAPred, the training datasets, the testing datasets and the selected features are freely available.

PmiRKB- plant micrRNA knowledge base
http://bis.zju.edu.cn/pmirkb/

Bioinformatic resource on plant microRNA that can be accessed under four broad domains: SNP module, Pri-miR module, MiR-Tar module, and Self-reg module.

Meng Y, Gou L, Chen D, Mao C, Jin Y, Wu P, Chen M. PmiRKB: a plant microRNA knowledge base. Nucleic Acids Res. 2011 Jan;39(Database issue):D181-7. Epub 2010 Aug 18. PubMed PMID: 20719744; PubMed Central PMCID: PMC3013752.

2011

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PMRD- Plant microRNA database
http://bioinformatics.cau.edu.cn/PMRD/

Database on plant microRNA obtained from in-house data and public repositories and contains sequence information, secondary structure, target genes, expression profiles and a genome browser.

Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z. PMRD: plant microRNA database. Nucleic Acids Res. 2010 Jan;38(Database issue):D806-13. Epub 2009 Oct 6. PubMed PMID: 19808935; PubMed Central PMCID: PMC2808885.

2010

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Predictions are downloadable
Predictions are downloadable

pssRNAMiner
http://bioinfo3.noble.org/pssRNAMiner/

A web server which identifies trans-acting siRNA clusters in plants, including their regulatory components.

Dai X, Zhao PX. pssRNAMiner: a plant short small RNA regulatory cascade analysis server. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W114-8. Epub 2008 May 12. PubMed PMID: 18474525; PubMed Central PMCID: PMC2447807.

2008

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Open access.
Open access.

SoMART
http://somart.ist.berkeley.edu/

Database on plant microRNA and trans acting small interfering RNA.

Li F, Orban R, Baker B. SoMART: a web server for plant miRNA, tasiRNA and target gene analysis. Plant J. 2012 Jan 24. doi: 10.1111/j.1365-313X.2012.04922.x. [Epub ahead of print] PubMed PMID: 22268718.

2012

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SplamiR
http://www.uni-jena.de/SplamiR.html

Bioinformatic tool for identification of spliced microRNAs in a given target plant mRNA.

Thieme CJ, Gramzow L, Lobbes D, Theissen G. SplamiR--prediction of spliced miRNAs in plants. Bioinformatics. 2011 May 1;27(9):1215-23. Epub 2011 Mar 17. PubMed PMID: 21421552.

2011

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To be validated
To be validated

TAPIR- target prediction for plant microRNAs
http://bioinformatics.psb.ugent.be/webtools/tapir

Bioinformatic tool for determining plant microRNA targets.

Bonnet E, He Y, Billiau K, Van de Peer Y. TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics. 2010 Jun 15;26(12):1566-8. Epub 2010 Apr 28. PubMed PMID: 20430753.

2010

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Target-align
http://www.leonxie.com/targetAlign.php

Bioinformatic tool for prediction of plant microRNA targets based on Smith-Waterman-like alignment tool.

Xie F, Zhang B. Target-align: a tool for plant microRNA target identification. Bioinformatics. 2010 Dec 1;26(23):3002-3. Epub 2010 Oct 7. PubMed PMID: 20934992.

2010

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WMD3- Web microRNA designer
http://wmd3.weigelworld.org/cgi-bin/webapp.cgi?page=Home;project=stdwmd

Web based tool that was developed to assist a user in the designing of artificial microRNAs.

Ossowski S, Schwab R, Weigel D. Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J. 2008 Feb;53(4):674-90. Review. PubMed PMID: 18269576

2008

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Open access ( GNU General Public License (GPL) )
Open access ( GNU General Public License (GPL) )