Supplementary table 1: Database list

 

miRNA Sequence and Annotation Resource

Resource

Organism

Main feature

Unique features

URL

Reference

miRBase

Any

miRNA sequences

and annotations

Stem loop structure and deep sequencing

Search miRNAs by genomic location

Search of miRNA clusters

Search of homolog miRNAs in other species

 

http://www.mirbase.org/

[1]

CoGemiR

Animals

Comparative genomic analysis of miRNAs

Pre-miRNA and mature sequence

Expression data in different tissues

Tissue specificity

 

http://cogemir.tigem.it/

\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>CoGemiR: a comparative genomics microRNA database</title><secondary-title>BMC Genomics</secondary-title><alt-title>BMC genomics</alt-title></titles><periodical><full-title>BMC Genomics</full-title><abbr-1>BMC genomics</abbr-1></periodical><alt-periodical><full-title>BMC Genomics</full-title><abbr-1>BMC genomics</abbr-1></alt-periodical><pages>457</pages><volume>9</volume><keywords><keyword>Animals</keyword><keyword>Computational Biology</keyword><keyword>Database Management Systems</keyword><keyword>*Databases, Nucleic Acid</keyword><keyword>*Genomics</keyword><keyword>MicroRNAs/*genetics</keyword><keyword>Sequence Analysis, RNA</keyword><keyword>*User-Computer Interface</keyword></keywords><dates><year>2008</year></dates><isbn>1471-2164 (Electronic)&#xD;1471-2164 (Linking)</isbn><accession-num>18837977</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/18837977</url></related-urls></urls><custom2>2567348</custom2><electronic-resource-num>10.1186/1471-2164-9-457</electronic-resource-num></record></Cite></EndNote>[2]

microRNAviewer

Any

Conservation of

miRNAs in species

miRNA alignment and finding mismatches

miRNA genomic location

 

http://people.csail.mit.edu/akiezun/microRNAviewer/

\n This email address is being protected from spambots. You need JavaScript enabled to view it. .</auth-address><titles><title>miRviewer: a multispecies microRNA homologous viewer</title><secondary-title>BMC Res Notes</secondary-title><alt-title>BMC research notes</alt-title></titles><periodical><full-title>BMC Res Notes</full-title><abbr-1>BMC research notes</abbr-1></periodical><alt-periodical><full-title>BMC Res Notes</full-title><abbr-1>BMC research notes</abbr-1></alt-periodical><pages>92</pages><volume>5</volume><dates><year>2012</year></dates><isbn>1756-0500 (Electronic)&#xD;1756-0500 (Linking)</isbn><accession-num>22330228</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/22330228</url></related-urls></urls><custom2>3292992</custom2><electronic-resource-num>10.1186/1756-0500-5-92</electronic-resource-num></record></Cite></EndNote>[3]

miRiadne

Human

miRNA annotation

A tool for re-annotating miRNA name lists or datasets

 

http://www.miriadne.org/

[4]

miRNAfe

Any

RNA sequences features

A tool for RNA sequences features extraction

http://fich.unl.edu.ar/sinc/blog/web-demo/mirnafe/

\n This email address is being protected from spambots. You need JavaScript enabled to view it. .&#xD;Research Center for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL, CONICET, Ciudad Universitaria UNL, 3000 Santa Fe, Argentina.&#xD;Instituto de Investigaciones en Microbiologia y Parasitologia Medica (UBA), CONICET, Paraguay 2155, piso 13, 1121, Buenos Aires, Argentina.</auth-address><titles><title>miRNAfe: A comprehensive tool for feature extraction in microRNA prediction</title><secondary-title>Biosystems</secondary-title><alt-title>Bio Systems</alt-title></titles><periodical><full-title>Biosystems</full-title><abbr-1>Bio Systems</abbr-1></periodical><alt-periodical><full-title>Biosystems</full-title><abbr-1>Bio Systems</abbr-1></alt-periodical><pages>1-5</pages><volume>138</volume><dates><year>2015</year><pub-dates><date>Dec</date></pub-dates></dates><isbn>1872-8324 (Electronic)&#xD;0303-2647 (Linking)</isbn><accession-num>26499212</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/26499212</url></related-urls></urls><electronic-resource-num>10.1016/j.biosystems.2015.10.003</electronic-resource-num></record></Cite></EndNote>[5]

mirNEST

Any

miRNA sequence with integrative approach

Collection of animal, plant and virus microRNAs

miRNA prediction based on EST data

Integration with 13 resources include miRNA expression, polymorphisms and targets

 

http://rhesus.amu.edu.pl/mirnest/copy/

[6]

miROrtho

Any

Conservation of

miRNAs in species

Genomic location both known and predicted miRNAs

Ortholog multiple alignments

RNA secondary structure conservation

http://cegg.unige.ch/mirortho

[7]

mirvar

Human

Genetic variations in microRNAs

Genetic variants of miRNAs and its functional results

http://genome.igib.res.in/mirlovd

[8]

mirpub

Any

Search for publications related to microRNAs

Information about the correlation of microRNAs to any diseases, tissues and genes

http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=mirpub

[9]

miTRATA

Any

3′ modifications of microRNAs

Analysis of 3′ modifications of microRNAs

Including the loss or gain of nucleotides relative to the canonical sequence

 

https://wasabi.ddpsc.org/~apps/ta/

[10]

PNRD

Plant

miRNA and ncRNA basic information

Including literature mining, experimental targets, predicted targets, miRNA-ncRNA interaction, miRNA expression

 

http://structuralbiology.cau.edu.cn/PNRD/

\n This email address is being protected from spambots. You need JavaScript enabled to view it. .</auth-address><titles><title>PNRD: a plant non-coding RNA database</title><secondary-title>Nucleic Acids Res</secondary-title><alt-title>Nucleic acids research</alt-title></titles><periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></periodical><alt-periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></alt-periodical><pages>D982-9</pages><volume>43</volume><number>Database issue</number><keywords><keyword>*Databases, Nucleic Acid</keyword><keyword>Genomics</keyword><keyword>Internet</keyword><keyword>MicroRNAs/metabolism</keyword><keyword>RNA, Plant/chemistry/genetics/*metabolism</keyword><keyword>RNA, Untranslated/chemistry/genetics/*metabolism</keyword><keyword>Transcriptome</keyword></keywords><dates><year>2015</year><pub-dates><date>Jan</date></pub-dates></dates><isbn>1362-4962 (Electronic)&#xD;0305-1048 (Linking)</isbn><accession-num>25398903</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/25398903</url></related-urls></urls><custom2>4383960</custom2><electronic-resource-num>10.1093/nar/gku1162</electronic-resource-num></record></Cite></EndNote>[11]

VIRmiRNA

Virus

Experimentally validated viral miRNAs

Including  VIRmiRNA,  VIRmiRtar and  AVIRmir subdatabases

VIRmiRNA includes 1308 experimentally validated miRNA sequences with their isomiRs encoded by 44 viruses in viral miRNA

http://crdd.osdd.net/servers/virmirna/

[12]

WMD3

Plant

Automated design of artificial plant microRNAs

Platform requires only selection of favorite candidates according to a small set of criteria

http://wmd3.weigelworld.org/cgi-bin/webapp.cgi?page=

Home;project=stdwmd

[13]

Resources for Prediction of miRNA in A Sequence

Resource

Organism

Main feature

Unique features

URL

Reference

CID-miRNA

Human

Identification of

miRNAs in a sequence

 

Identification is based on secondary structure filtering systems

http://mirna.jnu.ac.in/cidmirna/

[14]

deepSOM

Animal

Plant

Identification of

miRNAs in a sequence

Machine learning tool for novel miRNA precursor prediction in genome-wide data

 

http://fich.unl.edu.ar/sinc/blog/web-demo/deepsom/

[15]

MapMI

Any

Recognition of

miRNAs in a sequence

Recognition is based on mapping validated miRNAs in one species to their most likely orthologous in other species

 

http://www.ebi.ac.uk/enright-srv/MapMi/

[16]

MatureBayes

Human

Mouse

Finding a mature miRNA

in sequence

Finding mature miRNA within a miRNA precursor

Identification is based on the sequence and secondary structures

http://mirna.imbb.forth.gr/MatureBayes.html

[17]

microPred

Human

Identification of a pre-miRNA in sequence

Human pre-miRNA prediction with high sensitivity and specificity

http://www.cs.ox.ac.uk/people/manohara.rukshan.batuwita/microPred.htm

\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>microPred: effective classification of pre-miRNAs for human miRNA gene prediction</title><secondary-title>Bioinformatics</secondary-title><alt-title>Bioinformatics</alt-title></titles><periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></periodical><alt-periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></alt-periodical><pages>989-95</pages><volume>25</volume><number>8</number><keywords><keyword>Animals</keyword><keyword>Base Sequence</keyword><keyword>Computational Biology/*methods</keyword><keyword>Databases, Genetic</keyword><keyword>Humans</keyword><keyword>MicroRNAs/chemistry/*classification/*genetics</keyword><keyword>Molecular Sequence Data</keyword><keyword>Nucleic Acid Conformation</keyword><keyword>RNA Precursors/chemistry/*classification/*genetics</keyword><keyword>Sequence Analysis, RNA/methods</keyword><keyword>*Software</keyword></keywords><dates><year>2009</year><pub-dates><date>Apr 15</date></pub-dates></dates><isbn>1367-4811 (Electronic)&#xD;1367-4803 (Linking)</isbn><accession-num>19233894</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/19233894</url></related-urls></urls><electronic-resource-num>10.1093/bioinformatics/btp107</electronic-resource-num></record></Cite></EndNote>[18]

Micro-pro SVM

Human

Recognition of

miRNAs in a sequence

Recognition of miRNA based on Drosha cleavage sites on a sequence

https://demo1.interagon.com/miRNA/cgi-bin/MicroprocessorSVM.cgi

[19]

MiPred

Human

Recognition of

miRNAs in a sequence

Distinguish the real pre-miRNAs from other hairpin sequences with similar stem-loops

http://www.bioinf.seu.edu.cn/miRNA/

[20]

Mir-abela

Human

Mouse

Rat

 

Identification of clustered microRNAs

Discovery of novel miRNAs based on the theory that many miRNAs occur in clusters

http://www.mirz.unibas.ch/cgi/pred_miRNA_genes.cgi

[21]

Miralign

Animal

Plant

Identification of

miRNAs in a sequence

Finding new miRNAs using structural similarity and sequence conservations

 

bioinfo.au.tsinghua.edu.cn/miralign

[22]

miRClassify

Any

Identification of

miRNAs in a sequence

A machine learning-based web server that can rapidly identify miRNA from the primary sequence

 

http://server.malab.cn/miRClassify/

[23]

MirEval 2.0

Any

Recognition of

miRNAs in a sequence

Finding new miRNAs based on secondary structure and conservation analysis

 

http://mimirna.centenary.org.au/mireval/

\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>Mireval: a web tool for simple microRNA prediction in genome sequences</title><secondary-title>Bioinformatics</secondary-title><alt-title>Bioinformatics</alt-title></titles><periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></periodical><alt-periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></alt-periodical><pages>1394-6</pages><volume>24</volume><number>11</number><keywords><keyword>*Algorithms</keyword><keyword>Base Sequence</keyword><keyword>Chromosome Mapping/*methods</keyword><keyword>*Internet</keyword><keyword>MicroRNAs/*genetics</keyword><keyword>Molecular Sequence Data</keyword><keyword>Sequence Analysis, RNA/*methods</keyword><keyword>*Software</keyword><keyword>*User-Computer Interface</keyword></keywords><dates><year>2008</year><pub-dates><date>Jun 1</date></pub-dates></dates><isbn>1367-4811 (Electronic)&#xD;1367-4803 (Linking)</isbn><accession-num>18453555</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/18453555</url></related-urls></urls><electronic-resource-num>10.1093/bioinformatics/btn137</electronic-resource-num></record></Cite></EndNote>[24]

miRNA-dis

Any

Recognition of

miRNAs in a sequence

 

MicroRNA precursor identification based on distance structure status pairs

http://bioinformatics.hitsz.edu.cn/miRNA-dis/

\n This email address is being protected from spambots. You need JavaScript enabled to view it. This email address is being protected from spambots. You need JavaScript enabled to view it. This email address is being protected from spambots. You need JavaScript enabled to view it. This email address is being protected from spambots. You need JavaScript enabled to view it. This email address is being protected from spambots. You need JavaScript enabled to view it. .</auth-address><titles><title>miRNA-dis: microRNA precursor identification based on distance structure status pairs</title><secondary-title>Mol Biosyst</secondary-title><alt-title>Molecular bioSystems</alt-title></titles><periodical><full-title>Mol Biosyst</full-title><abbr-1>Molecular bioSystems</abbr-1></periodical><alt-periodical><full-title>Mol Biosyst</full-title><abbr-1>Molecular bioSystems</abbr-1></alt-periodical><pages>1194-204</pages><volume>11</volume><number>4</number><keywords><keyword>Animals</keyword><keyword>Computational Biology/*methods</keyword><keyword>Databases, Genetic</keyword><keyword>Humans</keyword><keyword>Internet</keyword><keyword>MicroRNAs/*chemistry/*genetics</keyword><keyword>RNA, Plant</keyword><keyword>RNA, Viral</keyword><keyword>*User-Computer Interface</keyword></keywords><dates><year>2015</year><pub-dates><date>Apr</date></pub-dates></dates><isbn>1742-2051 (Electronic)&#xD;1742-2051 (Linking)</isbn><accession-num>25715848</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/25715848</url></related-urls></urls><electronic-resource-num>10.1039/c5mb00050e</electronic-resource-num></record></Cite></EndNote>[25]

miRNAFold

Any

Recognition of

miRNAs in a sequence

 

Ab initio miRNA  precursor prediction in genomes

https://evryrna.ibisc.univ-evry.fr/miRNAFold/

\n This email address is being protected from spambots. You need JavaScript enabled to view it. .</auth-address><titles><title>miRNAFold: a web server for fast miRNA precursor prediction in genomes</title><secondary-title>Nucleic Acids Res</secondary-title><alt-title>Nucleic acids research</alt-title></titles><periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></periodical><alt-periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></alt-periodical><dates><year>2016</year><pub-dates><date>May 29</date></pub-dates></dates><isbn>1362-4962 (Electronic)&#xD;0305-1048 (Linking)</isbn><accession-num>27242364</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/27242364</url></related-urls></urls><electronic-resource-num>10.1093/nar/gkw459</electronic-resource-num></record></Cite></EndNote>[26]

miRNAminer

Vertebrates

Finding homologous

miRNA genes

 

Identifying conserved homolog miRNA genes

Analyzing 10 vertebrates

http://groups.csail.mit.edu/pag/mirnaminer/

\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>miRNAminer: a tool for homologous microRNA gene search</title><secondary-title>BMC Bioinformatics</secondary-title><alt-title>BMC bioinformatics</alt-title></titles><periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></periodical><alt-periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></alt-periodical><pages>39</pages><volume>9</volume><keywords><keyword>Animals</keyword><keyword>Base Sequence</keyword><keyword>Cattle</keyword><keyword>Databases, Genetic/trends</keyword><keyword>Dogs</keyword><keyword>Humans</keyword><keyword>Internet/trends</keyword><keyword>Mice</keyword><keyword>MicroRNAs/analysis/*genetics</keyword><keyword>Molecular Sequence Data</keyword><keyword>Opossums</keyword><keyword>Pan troglodytes</keyword><keyword>Rats</keyword><keyword>*Sequence Homology, Nucleic Acid</keyword></keywords><dates><year>2008</year></dates><isbn>1471-2105 (Electronic)&#xD;1471-2105 (Linking)</isbn><accession-num>18215311</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/18215311</url></related-urls></urls><custom2>2258288</custom2><electronic-resource-num>10.1186/1471-2105-9-39</electronic-resource-num></record></Cite></EndNote>[27]

miRNA SVM

Human

Identification of

miRNAs in a sequence

Suggesting microRNAs by a classifier that predicts 5´

Drosha processing sites in hairpins that are candidate miRNAs

https://demo1.interagon.com/miRNA/cgi-bin/MiRNASVM.cgi

[19]

miRNAfinder &

 target Search

Human

Mouse

Rat

Recognition of

miRNAs in a sequence

Finding microRNA candidates in a sequence

display target expression

http://genome.ewha.ac.kr/miRNAexpress/

 

miRQuest

Human

Plant

Recognition of

miRNAs in a sequence

miRNA prediction interface which integrates four main tools

A benchmarking function to identify which one of the four integrated tools is more suitable for the species of interest

 

http://mirquest.integrativebioinformatics.me/index.php

[28]

MiRscan

Worm

Identification of

miRNAs in a sequence

 

Prediction based on sequence conservation and structural conformation

http://genes.mit.edu/mirscan/

[29]

PlantMiRNAPred

Plant

Identification of

miRNAs in a sequence

Classify real plant pre-miRNAs and pseudo hairpins

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

[30]

ProMiR II

Mammals

Fly

Worm

Recognition of

miRNAs in a sequence

Conserved, non-conserved, clustered, non-clustered miRNA prediction

Incorpating stem-loop filter and conservation score filter 

Consists of three programs: ProMiR-v, ProMiR-c and ProMiR-g

 

https://bi.snu.ac.kr/Research/ProMiR/ProMiR.html

[31]

psRobot

Plant

Analyze batch of plant small RNA data

Stem-loop small RNA prediction

Small RNA target prediction

 

http://omicslab.genetics.ac.cn/psRobot/

[32]

SSCprofiler

Human

Identification of

miRNAs in a sequence

Predicting putative miRNA genes based on sequence, structure and conservation

Scanning by entering chromosome number and start and end nucleotide

http://mirna.imbb.forth.gr/SSCprofiler.html

[33]

Vir-Mir db

Viruses

miRNA identification

Prediction of viral miRNA candidate hairpins

http://alk.ibms.sinica.edu.tw

[34]

miRNA Target Prediction Resources

Single Resource Target Prediction

Resource

Organism

Main feature

Unique features

URL

Reference

TargetScan

Mammals

Fly

Worm

miRNA target prediction

Finding broadly conserved, conserved and poorly conserved microRNA families

Showing miRNA position on gene

Alignment of miRNA target site in different organisms

http://www.targetscan.org

[35]

Bi-Targeting

Human

Viral and host miRNAs cooperatively regulate host gene expression

Viral and host miRNAs that cooperate in gene regulation

Integrate miRNA-target binding information,

miRNA expression profiles and GO annotations

 

www.cs.bgu.ac.il/~vaksler/BiTargeting.htm

\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>Gene bi-targeting by viral and human miRNAs</title><secondary-title>BMC Bioinformatics</secondary-title><alt-title>BMC bioinformatics</alt-title></titles><periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></periodical><alt-periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></alt-periodical><pages>249</pages><volume>11</volume><keywords><keyword>*Algorithms</keyword><keyword>Gene Regulatory Networks</keyword><keyword>Herpesvirus 4, Human/genetics</keyword><keyword>Humans</keyword><keyword>MicroRNAs/*genetics</keyword><keyword>RNA Processing, Post-Transcriptional</keyword><keyword>RNA, Messenger/*genetics</keyword><keyword>RNA, Viral/*genetics</keyword></keywords><dates><year>2010</year></dates><isbn>1471-2105 (Electronic)&#xD;1471-2105 (Linking)</isbn><accession-num>20465802</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/20465802</url></related-urls></urls><custom2>3583137</custom2><electronic-resource-num>10.1186/1471-2105-11-249</electronic-resource-num></record></Cite></EndNote>[36]

comTAR

Plant

miRNA target prediction

Analyze the variations of known miRNA targets during evolution

 

http://rnabiology.ibr-conicet.gov.ar/comtar/home

[37]

DIANA-LncBase

 

Human

Mouse

miRNA targets on long non-coding RNAs

Computationally predicted and experimentally validated results

Genomic locations

 

 

 

DIANA-LncBase

v2

Human

Mouse

miRNA targets on long non-coding RNAs

Computationally predicted and experimentally validated results

Genomic locations

 

www.microrna.gr/LncBase

[38]

DIANA-microT

V.4

Human

Mouse

miRNA target prediction

Finding targets based on miRNAs, genes or miRNA and gene

Link to KEGG, UniProt and iHOP

present predictions of TargetScan or Pictar or verification of TarBase

Conservation of target sites in different species

http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microtv4/index

[39]

DIANA-microT-CDS V.5

Human

Mouse

Worm

Fly

miRNA target prediction

Finding targets of a miRNAs based on miRNAs, genes or KEGG descriptions

Present predictions of TargetScan, Miranda or verification of TarBase

Conservation of target sites in different species

http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/index

[40]

EIMMo

Human

Mouse

Rat

Fish

Worm

Fly

miRNA target prediction

Target prediction for mRNAs in subsets of transcripts or different tissue or cell type

Alignment of multiple genomes in region of predated target site

Link to smiRNAdb samples that expression of selected miRNA is high 

 

http://www.mirz.unibas.ch/ElMMo3/

[41]

GUUGle

Any

miRNA target prediction

Locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs

 

http://bibiserv.techfak.uni-bielefeld.de/guugle

[42]

HomoloMTI

Mammals

 

Homology of miRNA target prediction

Identifying miRNA target sites on conserved sequences among several species

Integrated three resources, miRTarBase, miRBase and HomoloGene

http://homolomti.mbc.nctu.edu.tw/php/

 

mBISON

Human

Mouse

miRNA target prediction

Calculates the significance of over-representation of miRNA targets in a given non-ranked gene set

http://cbdm.mdc-berlin.de/~mgebhardt/cgi-bin/mbison/home/

[43]

MAMI

Human

miRNA target prediction

Specificity and sensitivity tuning for prediction

 

http://mami.med.harvard.edu

 

MicroCosm

Any

miRNA target prediction

Microcosm is basically derived from miRBase resource targets

Search by gene or miRNA name, GO term or keyword

Alignment of multiple genomes in region of predated target site

 

http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/

\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>miRBase: tools for microRNA genomics</title><secondary-title>Nucleic Acids Res</secondary-title><alt-title>Nucleic acids research</alt-title></titles><periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></periodical><alt-periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></alt-periodical><pages>D154-8</pages><volume>36</volume><number>Database issue</number><keywords><keyword>Animals</keyword><keyword>*Databases, Nucleic Acid</keyword><keyword>Gene Silencing</keyword><keyword>*Genomics</keyword><keyword>Humans</keyword><keyword>Internet</keyword><keyword>Mice</keyword><keyword>MicroRNAs/chemistry/*genetics</keyword><keyword>RNA, Messenger/metabolism</keyword><keyword>Software</keyword><keyword>Terminology as Topic</keyword></keywords><dates><year>2008</year><pub-dates><date>Jan</date></pub-dates></dates><isbn>1362-4962 (Electronic)&#xD;0305-1048 (Linking)</isbn><accession-num>17991681</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/17991681</url></related-urls></urls><custom2>2238936</custom2><electronic-resource-num>10.1093/nar/gkm952</electronic-resource-num></record></Cite></EndNote>[44]

microInspector

Any

Plant

 

miRNA binding sites

Finding miRNA binding sites in a target sequence

Analysis a user-defined RNA sequence

http://bioinfo1.uni-plovdiv.bg/cgi-bin/microinspector/

[45]

microRNA.org

Human

Mouse

Rat

Worm

Fly

miRNA target prediction

miRNA target prediction using miRanda algorithm

Search available for mRNA or miRNA

Showing miRNA-mRNA interaction

http://www.microrna.org

[46]

miRcode

Human

Whole transcriptome

miRNA target prediction

Target prediction for mRNA, LncRNA and pseudogene

Including 5´ UTR's , coding regions and 3´ UTR's

http://www.mircode.org

[47]

miRDB

Human

Mouse

Rat

Dog Chicken

 

miRNA target prediction

and functional annotation

miRNA target prediction using miRanda algorithm

Search for multiple miRNAs or genes

www.mirdb.org/

\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>miRDB: a microRNA target prediction and functional annotation database with a wiki interface</title><secondary-title>RNA</secondary-title><alt-title>Rna</alt-title></titles><periodical><full-title>RNA</full-title><abbr-1>Rna</abbr-1></periodical><alt-periodical><full-title>RNA</full-title><abbr-1>Rna</abbr-1></alt-periodical><pages>1012-7</pages><volume>14</volume><number>6</number><keywords><keyword>Animals</keyword><keyword>Base Sequence</keyword><keyword>*Computational Biology</keyword><keyword>*Databases, Nucleic Acid</keyword><keyword>Dogs</keyword><keyword>Humans</keyword><keyword>Mice</keyword><keyword>MicroRNAs/*physiology</keyword><keyword>Molecular Sequence Data</keyword><keyword>*Online Systems</keyword><keyword>Rats</keyword><keyword>*Software</keyword></keywords><dates><year>2008</year><pub-dates><date>Jun</date></pub-dates></dates><isbn>1469-9001 (Electronic)&#xD;1355-8382 (Linking)</isbn><accession-num>18426918</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/18426918</url></related-urls></urls><custom2>2390791</custom2><electronic-resource-num>10.1261/rna.965408</electronic-resource-num></record></Cite></EndNote>[48]

MirEE

Human

Mouse

Worm

miRNA target prediction

 

miRNA target prediction using an Ab-initio module followed

by a SVM module

http://eda.polito.it/miREE/

\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>miREE: miRNA recognition elements ensemble</title><secondary-title>BMC Bioinformatics</secondary-title><alt-title>BMC bioinformatics</alt-title></titles><periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></periodical><alt-periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></alt-periodical><pages>454</pages><volume>12</volume><keywords><keyword>Animals</keyword><keyword>*Artificial Intelligence</keyword><keyword>Gene Expression Regulation</keyword><keyword>Humans</keyword><keyword>MicroRNAs/*genetics/metabolism</keyword><keyword>RNA, Messenger/metabolism</keyword><keyword>*Regulatory Sequences, Ribonucleic Acid</keyword><keyword>Sensitivity and Specificity</keyword><keyword>Software</keyword><keyword>Support Vector Machines</keyword></keywords><dates><year>2011</year></dates><isbn>1471-2105 (Electronic)&#xD;1471-2105 (Linking)</isbn><accession-num>22115078</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/22115078</url></related-urls></urls><custom2>3265527</custom2><electronic-resource-num>10.1186/1471-2105-12-454</electronic-resource-num></record></Cite></EndNote>[49]

miRMaid

Any

Integrating miRNA data sources

Integrating miRNA data sources and developing an interface for computer programming

 

http://current.mirmaid.org/

\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>miRMaid: a unified programming interface for microRNA data resources</title><secondary-title>BMC Bioinformatics</secondary-title><alt-title>BMC bioinformatics</alt-title></titles><periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></periodical><alt-periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></alt-periodical><pages>29</pages><volume>11</volume><keywords><keyword>Computational Biology/*methods</keyword><keyword>Databases, Genetic</keyword><keyword>MicroRNAs/*chemistry</keyword><keyword>*Programming Languages</keyword><keyword>Sequence Analysis, RNA</keyword><keyword>*Software</keyword></keywords><dates><year>2010</year></dates><isbn>1471-2105 (Electronic)&#xD;1471-2105 (Linking)</isbn><accession-num>20074352</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/20074352</url></related-urls></urls><custom2>2831003</custom2><electronic-resource-num>10.1186/1471-2105-11-29</electronic-resource-num></record></Cite></EndNote>[50]

miRmap

Mammals

Fish

miRNA target prediction

Prediction of microRNA target repression strength

Including 5´ UTR's , coding regions and 3´ UTR's

http://mirmap.ezlab.org/

[51]

miRNA_Targets

 

Fish

Worm

Fly

miRNA target prediction

 

Target prediction using miRanda and RNAhybrid algorithms on

mRNA 5´ UTR's , coding regions and 3´ UTR's

http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html

[52]

MirTif

Any

miRNA target interaction filter

A post-processing filter for the miRNA: gene hybrids prediction of various algorithms

 

http://bsal.ym.edu.tw/mirtif

\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>MiRTif: a support vector machine-based microRNA target interaction filter</title><secondary-title>BMC Bioinformatics</secondary-title><alt-title>BMC bioinformatics</alt-title></titles><periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></periodical><alt-periodical><full-title>BMC Bioinformatics</full-title><abbr-1>BMC bioinformatics</abbr-1></alt-periodical><pages>S4</pages><volume>9 Suppl 12</volume><keywords><keyword>3&apos; Untranslated Regions</keyword><keyword>Algorithms</keyword><keyword>Area Under Curve</keyword><keyword>Artificial Intelligence</keyword><keyword>Computational Biology/methods</keyword><keyword>Computer Simulation</keyword><keyword>Computers</keyword><keyword>False Positive Reactions</keyword><keyword>Humans</keyword><keyword>MicroRNAs/*genetics/metabolism</keyword><keyword>Pattern Recognition, Automated/methods</keyword><keyword>Reproducibility of Results</keyword><keyword>Sensitivity and Specificity</keyword><keyword>Sequence Analysis, RNA/methods</keyword><keyword>Software</keyword></keywords><dates><year>2008</year></dates><isbn>1471-2105 (Electronic)&#xD;1471-2105 (Linking)</isbn><accession-num>19091027</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/19091027</url></related-urls></urls><custom2>2638144</custom2><electronic-resource-num>10.1186/1471-2105-9-S12-S4</electronic-resource-num></record></Cite></EndNote>[53]

MtiBase

Human

Mouse

miRNA-target interactions database

Identify CDS-located and 5'UTR-located miRNA binding sites Systematically evaluate miRNA regulatory effects on mRNA stability and translation

http://mtibase.sysu.edu.cn/index.php

[54]

MultiMiTar

Any

miRNA target prediction

Target prediction with multi-objective feature selection

http://www.isical.ac.in/~bioinfo_miu/multimitar.htm

[55]

NBmiRTar

Any

miRNA target prediction

Target prediction based on NbmiRTar algorithm

http://wotan.wistar.upenn.edu/NBmiRTar

[56]

Patrocles

Vertebrates

Polymorphisms affect gene regulation

DNA polymorphisms predicted to affect miRNA-gene control 

http://www.patrocles.org/

[57]

PicTar

Vertebrate Nematode

Fly

miRNA target prediction

Target prediction based on PicTar algorithm

Multiple sequence alignment in region of predated target site

http://pictar.mdc-berlin.de/

[58]

P-TAREF

Plant

miRNA target prediction

Refines the process of microRNA target identification through incorporation of local interaction information

 

http://scbb.ihbt.res.in/new/p-taref/form1.html

[59]

repTar

Human

Mouse

 

miRNA target prediction

Target prediction in human, mouse and several cellular targets of viral miRNAs

http://reptar.ekmd.huji.ac.il.

[60]

RNA22 v2

Human

Mouse

Fly

Worm

miRNA target prediction

Identifying microRNA binding sites and their corresponding heteroduplexes

Access pre-computed rna22 target predictions for multiple species

http://cm.jefferson.edu/rna22/Precomputed/

[61]

STarMir

Human

Mouse

Worm

 

miRNA binding sites

Finding miRNA binding sites in a target sequence

Analysis a user-defined RNA sequence

http://sfold.wadsworth.org/cgi-bin/starmir.pl

\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>Sfold web server for statistical folding and rational design of nucleic acids</title><secondary-title>Nucleic Acids Res</secondary-title><alt-title>Nucleic acids research</alt-title></titles><periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></periodical><alt-periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></alt-periodical><pages>W135-41</pages><volume>32</volume><number>Web Server issue</number><keywords><keyword>Algorithms</keyword><keyword>Computational Biology</keyword><keyword>Internet</keyword><keyword>Models, Statistical</keyword><keyword>Nucleic Acid Conformation</keyword><keyword>Oligonucleotides, Antisense/chemistry</keyword><keyword>RNA/*chemistry</keyword><keyword>RNA Stability</keyword><keyword>RNA, Catalytic/chemistry</keyword><keyword>RNA, Small Interfering/chemistry</keyword><keyword>*Software</keyword><keyword>User-Computer Interface</keyword></keywords><dates><year>2004</year><pub-dates><date>Jul 1</date></pub-dates></dates><isbn>1362-4962 (Electronic)&#xD;0305-1048 (Linking)</isbn><accession-num>15215366</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/15215366</url></related-urls></urls><custom2>441587</custom2><electronic-resource-num>10.1093/nar/gkh449</electronic-resource-num></record></Cite></EndNote>[62]

TargetMiner

Human

Mouse

Fly

 

miRNA target prediction

Target prediction with systematic identification of negative examples

http://www.isical.ac.in/~bioinfo_miu/targetminer20.htm

\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples</title><secondary-title>Bioinformatics</secondary-title><alt-title>Bioinformatics</alt-title></titles><periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></periodical><alt-periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></alt-periodical><pages>2625-31</pages><volume>25</volume><number>20</number><keywords><keyword>Animals</keyword><keyword>Artificial Intelligence</keyword><keyword>Computational Biology/*methods</keyword><keyword>Databases, Nucleic Acid</keyword><keyword>Humans</keyword><keyword>Internet</keyword><keyword>MicroRNAs/*chemistry</keyword><keyword>RNA, Messenger/chemistry</keyword><keyword>Sequence Analysis, RNA</keyword><keyword>*Software</keyword></keywords><dates><year>2009</year><pub-dates><date>Oct 15</date></pub-dates></dates><isbn>1367-4811 (Electronic)&#xD;1367-4803 (Linking)</isbn><accession-num>19692556</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/19692556</url></related-urls></urls><electronic-resource-num>10.1093/bioinformatics/btp503</electronic-resource-num></record></Cite></EndNote>[63]

TargetRank

Human

Mouse

miRNA target prediction

Targeting by endogenous and exogenous microRNAs and siRNAs

http://hollywood.mit.edu/targetrank

[64]

TargetRNA2

Bacteria

sRNA target prediction

Identifies mRNA targets of sRNA regulatory action in bacteria

http://cs.wellesley.edu/~btjaden/TargetRNA2/

\n This email address is being protected from spambots. You need JavaScript enabled to view it. .</auth-address><titles><title>TargetRNA2: identifying targets of small regulatory RNAs in bacteria</title><secondary-title>Nucleic Acids Res</secondary-title><alt-title>Nucleic acids research</alt-title></titles><periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></periodical><alt-periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></alt-periodical><pages>W124-9</pages><volume>42</volume><number>Web Server issue</number><keywords><keyword>Escherichia coli/genetics</keyword><keyword>Internet</keyword><keyword>Nucleic Acid Conformation</keyword><keyword>RNA, Bacterial/*chemistry/metabolism</keyword><keyword>RNA, Messenger/*chemistry/metabolism</keyword><keyword>RNA, Small Untranslated/*chemistry/metabolism</keyword><keyword>Sequence Analysis, RNA</keyword><keyword>*Software</keyword></keywords><dates><year>2014</year><pub-dates><date>Jul</date></pub-dates></dates><isbn>1362-4962 (Electronic)&#xD;0305-1048 (Linking)</isbn><accession-num>24753424</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/24753424</url></related-urls></urls><custom2>4086111</custom2><electronic-resource-num>10.1093/nar/gku317</electronic-resource-num></record></Cite></EndNote>[65]

TargetSpy

Human

Mouse

Rat

Chicken

Fly

miRNA target prediction

Target prediction based on scores without demanding a seed match

http://webclu.bio.wzw.tum.de/targetspy/index.php?down=true

[66]

VIRmiRNA

Virus

miRNA target prediction

Including  VIRmiRNA,  VIRmiRtar and  AVIRmir subdatabases

VIRmiRtar contains 7283 target genes of viral miRNAs

AVIRmir includes 542 antiviral miRNAs encoded by the host against 24 viruses

http://crdd.osdd.net/servers/virmirna/

[12]

Vita

Human

Mouse

Rat

Chicken

Virus

miRNA target prediction

Prediction of host miRNA targets in viruses

http://vita.mbc.nctu.edu.tw/

[67]

miRNA Target Prediction Resources

User Defined Sequence Resources

Resource

Organism

Main feature

Unique features

URL

Reference

RNAhybrid

Human

Worm

Fly

Hybridization of two RNA sequence

Searching the minimum free energy hybridization of two desired RNA sequences

http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/

[68]

IntaRNA

Any

Interaction prediction for

your own sequence

Prediction of interactions between two RNA molecules

http://rna.informatik.uni-freiburg.de/IntaRNA/Input.jsp

\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions</title><secondary-title>Bioinformatics</secondary-title><alt-title>Bioinformatics</alt-title></titles><periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></periodical><alt-periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></alt-periodical><pages>2849-56</pages><volume>24</volume><number>24</number><keywords><keyword>Computational Biology/*methods</keyword><keyword>Escherichia coli/genetics/metabolism</keyword><keyword>RNA, Bacterial/*chemistry</keyword><keyword>RNA, Messenger/chemistry</keyword><keyword>RNA, Untranslated/*chemistry</keyword><keyword>*Software</keyword></keywords><dates><year>2008</year><pub-dates><date>Dec 15</date></pub-dates></dates><isbn>1367-4811 (Electronic)&#xD;1367-4803 (Linking)</isbn><accession-num>18940824</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/18940824</url></related-urls></urls><custom2>2639303</custom2><electronic-resource-num>10.1093/bioinformatics/btn544</electronic-resource-num></record></Cite></EndNote>[69]

miRNA_Targets

Any

Interaction prediction for

your own sequence

Interaction prediction of a desired sequence and known miRNAs

Target prediction using miRanda and RNAhybrid algorithms on mRNA 5´ UTR's , coding regions and 3´ UTR's

 

http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html

[52]

MIRZA

Any

Interaction prediction for

your own sequence

A biophysical miRNA-mRNA interaction model based on  Argonaute 2 cross-linking and immunoprecipitation data

http://www.clipz.unibas.ch/index.php?r=tools/sub/mirza

 

[70]

MR-microT

Human

Mouse

Fly

 

Interaction prediction for

your own sequence

Provides near-real time predictions for custom miRNA sequences

http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=mrmicrot/index

\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>Functional microRNA targets in protein coding sequences</title><secondary-title>Bioinformatics</secondary-title><alt-title>Bioinformatics</alt-title></titles><periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></periodical><alt-periodical><full-title>Bioinformatics</full-title><abbr-1>Bioinformatics</abbr-1></alt-periodical><pages>771-6</pages><volume>28</volume><number>6</number><keywords><keyword>*3&apos; Untranslated Regions</keyword><keyword>Algorithms</keyword><keyword>Animals</keyword><keyword>Humans</keyword><keyword>MicroRNAs/chemistry/genetics/*metabolism</keyword><keyword>*Open Reading Frames</keyword><keyword>*Regulatory Sequences, Ribonucleic Acid</keyword></keywords><dates><year>2012</year><pub-dates><date>Mar 15</date></pub-dates></dates><isbn>1367-4811 (Electronic)&#xD;1367-4803 (Linking)</isbn><accession-num>22285563</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/22285563</url></related-urls></urls><electronic-resource-num>10.1093/bioinformatics/bts043</electronic-resource-num></record></Cite></EndNote>[71]

PITA

Human

Mouse

Fly

Worm

Interaction prediction for

your own sequence

Assessment of interactions between RNA sequences based on PITA algorithm

Using known miRNAs or user-provided miRNA sequences

http://genie.weizmann.ac.il/pubs/mir07/mir07_prediction.html

[72]

psRNATarget

Plant

miRNA target prediction

Reverse complementary matching between miRNA and target transcript using a proven scoring schema

Target site accessibility evaluation by calculating unpaired

energy

 

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

[73]

RNA22 v2

Human

Mouse

Fly

Worm

Interaction prediction for

your own sequence

Identifying microRNA binding sites and their corresponding heteroduplexes

Interaction prediction between a desired miRNA and target sequence

 

http://cm.jefferson.edu/rna22/Interactive/

[61]

TAPIR

Plant

miRNA target prediction

Search for plant miRNA targets using a fast and a precise algorithm

User defined score and free energy ratio

http://bioinformatics.psb.ugent.be/webtools/tapir/

[74]

miRNA Target Prediction Resources

Composite Target Prediction Resources

Resource

Organism

Main feature

Unique features

URL

Reference

miRWalk 2.0

Human

Mouse

Rat

User-friendly composite

target prediction resource

Combining miRNA target prediction results from DIANA-microT, miRanda, MirTarget2, RNAhybrid, PicTar4, PicTar5, PITA, RNA22, TargetScan and miRWalk

Search of binding sites within 5´ UTR, CDS and 3´UTR

Search in all or longer transcripts

Predicted targets are diagrammed to pathways and diseases

 

http://www.umm.uni-heidelberg.de/apps/zmf/mirwalk/

[75]

BcmicrO

Human

Composite target prediction resource

Combines the prediction of TargetScan, miRanda, PicTar, mirTarget, PITA, and Diana microT

 

http://compgenomics.utsa.edu/gene/gene_1.php

[76]

ComiR

Human

Mouse

Worm

Fly

Composite target prediction resource

Combining miRNA target prediction results from miRanda, PITA, TargetScan and mirSVR

Using miRNA expression to improve and combine multiple miRNA targets

 

http://www.benoslab.pitt.edu/comir/

\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>ComiR: Combinatorial microRNA target prediction tool</title><secondary-title>Nucleic Acids Res</secondary-title><alt-title>Nucleic acids research</alt-title></titles><periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></periodical><alt-periodical><full-title>Nucleic Acids Res</full-title><abbr-1>Nucleic acids research</abbr-1></alt-periodical><pages>W159-64</pages><volume>41</volume><number>Web Server issue</number><keywords><keyword>3&apos; Untranslated Regions</keyword><keyword>Algorithms</keyword><keyword>Animals</keyword><keyword>Caenorhabditis elegans/genetics</keyword><keyword>Drosophila melanogaster/genetics</keyword><keyword>Gene Expression Regulation</keyword><keyword>Humans</keyword><keyword>Internet</keyword><keyword>Mice</keyword><keyword>MicroRNAs/*metabolism</keyword><keyword>Polymorphism, Single Nucleotide</keyword><keyword>RNA, Messenger/chemistry/*metabolism</keyword><keyword>*Software</keyword></keywords><dates><year>2013</year><pub-dates><date>Jul</date></pub-dates></dates><isbn>1362-4962 (Electronic)&#xD;0305-1048 (Linking)</isbn><accession-num>23703208</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/23703208</url></related-urls></urls><custom2>3692082</custom2><electronic-resource-num>10.1093/nar/gkt379</electronic-resource-num></record></Cite></EndNote>[77]

HocTar

Human

Composite target prediction resource

Integrating miRNA target predictions of miRanda, TargetScan and PicTar

 

http://hoctar.tigem.it

\n This email address is being protected from spambots. You need JavaScript enabled to view it. </auth-address><titles><title>HOCTAR database: a unique resource for microRNA target prediction</title><secondary-title>Gene</secondary-title><alt-title>Gene</alt-title></titles><periodical><full-title>Gene</full-title><abbr-1>Gene</abbr-1></periodical><alt-periodical><full-title>Gene</full-title><abbr-1>Gene</abbr-1></alt-periodical><pages>51-8</pages><volume>480</volume><number>1-2</number><keywords><keyword>Computational Biology/methods</keyword><keyword>*Databases, Factual</keyword><keyword>*Gene Expression Regulation</keyword><keyword>Humans</keyword><keyword>*MicroRNAs</keyword><keyword>Reproducibility of Results</keyword></keywords><dates><year>2011</year><pub-dates><date>Jul 1</date></pub-dates></dates><isbn>1879-0038 (Electronic)&#xD;0378-1119 (Linking)</isbn><accession-num>21435384</accession-num><urls><related-urls><url>http://www.ncbi.nlm.nih.gov/pubmed/21435384</url></related-urls></urls><custom2>3113163</custom2><electronic-resource-num>10.1016/j.gene.2011.03.005</electronic-resource-num></record></Cite></EndNote>[78]

mirDIP

Human

Composite target prediction source

Merging microRNA predictions twelve microRNA prediction datasets from DIANA-microT, microcosm, miRanda, PicTar, PITA, RNA22 and TargetScan algorithms 

Finding signaling pathway-associated microRNAs

 

http://ophid.utoronto.ca/mirDIP/

[79]

miRecords

Mammals

Fish

Worm

Fly

Composite target prediction source for nine species

Combining of predicted miRNA targets produced by 11  algorithms DIANA-microT, MicroInspector, miRanda, MirTarget2, miTarget, NBmiRTar, PicTar, PITA, RNA22, RNAhybrid and TargetScan

Target predictions can be pooled with the validated interactions

 

http://c1.accurascience.com/miRecords/

[80]

miRGate

Human

Mouse

Rat

Composite target prediction resource

Using  miRanda, Pita, RNAHybrid, Microtar, TargetScan,  TarBase,  mirTarBase and  miRecords

Analyze miRNA and gene isoforms lists under a common and consistent space of annotations

 

http://mirgate.bioinfo.cnio.es/miRGate/

[81]

miRGator v3.0

Human

Composite target prediction resource

Joining the results of PicTar, TargetScan, miRanda, microcosm, PITA and miRDB algorithms

Containing microRNA diversity, expression profiles and target relationships

http://mirgator.kobic.re.kr/

[82]

miRNA body map

Human

Mouse

Rat

Composite target prediction resource

Integration of predicted miRNA targets produced by eight miRNA target algorithms PITA, DIANA-microT, Microcosm, RNA22, TargetScan, miRDB, TarBase and miRecords

miRNA function and their effect on pathways

 

http://mellfire.ugent.be/public/body_map/

[83]

miRNAMap 2.0

Human

Composite target prediction resource

Combining miRNA targeting results of Miranda, RNAHybrid  and TargetScan algorithms

 

http://mirnamap.mbc.nctu.edu.tw/

[84]

miRSystem

Human

Mouse

Composite target prediction resource

Combining miRNA targeting of  DIANA, miRanda, miRBridge, PicTar, PITA, rna22 and TargetScan  algorithms

 

http://mirsystem.cgm.ntu.edu.tw/index.php

[85]

mirTarPri

Human

Composite target prediction based on functional genomic data

Prioritizing candidate mirRNA targets in the context of

functional genomic data

Using  Gene Ontology and protein protein interaction networks

Provides mirRNA target list of TargetScan, PicTar, PITA,DIANA-microT, miRanda, RNAhybrid  tarBase, mirRecord and mir2Disease

 

http://www.bio-bigdata.com/mirTarPri/

[86]

miRò v 2.0

Human

Composite target prediction resource

Integration miRNA target predictions of miRanda, PicTar, TargetScan and miRecords algorithms

http://microrna.osumc.edu/miro/home/about?page_name=About

[87]

mirRor Suite