| deepBase |
A database for annotating and discovering small and long ncRNAs (microRNAs, siRNAs, piRNAs…) from high-throughput deep sequencing data. |
Both |
http://deepbase.sysu.edu.cn/
|
| DIANA-microT-CDS |
Thermodynamic modeling. |
Both |
http://diana.cslab.ece.ntua.gr/
|
| DIANA-mirGen 2.0 |
A database of microRNA genomic information and regulation. |
Both |
http://diana.cslab.ece.ntua.gr/mirgen/
|
| GenMiR++ |
Paired expression profiles of microRNAs and mRNAs; as well as Baynesian inference. |
Both |
http://www.psi.toronto.edu/genmir
|
| mimiRNA |
Expression correlation. |
Both |
http://mimirna.centenary.org.au
|
| mirBridge |
Complementary and target site conservation. |
Download |
http://mirbridge.org/
|
| miRanda |
Complementary and target site conservation. |
Both |
http://www.microrna.org
|
| miRBase |
A searchable database of published miRNA sequences and annotation. |
Both |
http://www.mirbase.org/
|
| miRDB |
Microarray corrleation training; as well as Support Vector Machine. |
Both |
http://mirdb.org
|
| miRecords |
Validated targets and algorithm integration. |
Both |
http://mirecords.biolead.org/doc.php
|
| miRGator |
Expression correlation and algorithm integration. |
Online Search |
http://mirgator.kobic.re.kr/
|
| miRGen |
Positional relationships target prediction integration. |
Both |
http://www.diana.pcbi.upenn.edu/miRGen.html
|
| miRNA-Target Gene Prediction at EMBL |
Complementary and target site conservation. |
Online Search |
http://www.russell.embl.de/miRNAs
|
| miRNAMap |
Genomic maps of microRNA genes and their target genes in mammalian genomes. |
Both |
http://mirnamap.mbc.nctu.edu.tw/
|
| MicroInspector |
Algorithm integration. |
Online Search |
http://bioinfo1.uni-plovdiv.bg/cgi-bin/microinspector/
|
| MiTarget |
Positional relationships thermodynamic modeling; as well as Support Vector Machine. |
Online Search |
http://cbit.snu.ac.kr/miTarget
|
| PicTar |
Target site conservation and thermodynamic modeling. |
Both |
http://pictar.mdc-berlin.de/
|
| PITA |
Incorporating the role of target site accessibility, as determined by base-pairing interactions within the mRNA, in microRNA target recognition. |
Both |
http://genie.weizmann.ac.il/
|
| PMRD |
PMRD: Plant microRNA database. |
Both |
http://bioinformatics.cau.edu.cn/PMRD/
|
| RepTar |
Searching for repeating 3′ UTR target sites. |
both |
http://reptar.ekmd.huji.ac.il/
|
| RNA22 |
Identifying patterns in cDNAs and matching to miRs. |
Online search |
http://cbcsrv.watson.ibm.com/rna22.html
|
| RNAhybrid |
Thermodynamics & statistical model. |
Both |
http://bibiserv.techfak.uni-bielefeld.de/rnahybrid
|
| starBase |
Argonaute CLIP-Seq and degradome sequencing data. |
Both |
http://starbase.sysu.edu.cn/
|
| TarBase |
Experimentally validated targets. |
Both |
http://diana.cslab.ece.ntua.gr/tarbase/
|
| TargetScan |
Seed complementary and target site conservation. |
Both |
http://www.targetscan.org
|
| ViTa |
Complementary of host microRNAs to viruses. |
Both |
http://vita.mbc.nctu.edu.tw/
|
