From BINF - Bioinformatics Centre
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Methods in microRNA bioinformatics
This page is supporting the article:
Principles of microRNA gene and target prediction Morten Lindow and Jan Gorodkin DNA and Cell Biology. 2007, 26(5): 339-351
Below, you can find extended and hyperlinked versions of Table 1 and 2 from the paper.
Target prediction
| Algorithm | Matching | Energy filter | Search space reduction | Scoring scheme | Downloadable program | Submit sequence for online search | Database of predictions |
|---|---|---|---|---|---|---|---|
| TargetScanS | Seed variations only | None | Whole genome alignments | All equal | No | No | Yes |
| miRanda | Weighted alignment emphasizing seed | RNAfold with linker hack | AVID alignment of UTRs | ad hoc | Yes | No | Yes (Yes) |
| PicTar | Seedmatch or compensatory | >33% of energy for perfect match of miRNA | Whole genome alignments | Maximum likelihood, combined for all sites meeting tresholds | No | No | Yes |
| RNAhybrid | Integrated match and energy | Guarantees to find lowest energy site | Not implemented | extreme value dist. BLAST-like evalue | Yes | Yes | No |
| Target Boost | Boosted genetic algorithm to create weighted sequence motifs that characterize the probable binding characteristics. | None | Not implemented | Yes | No | Demo only | No |
| Rna22 | Best alignment | None | 'Target Islands' with high density of pattern 'hits' | extreme value dist. BLAST-like evalue | No | Yes | No |
| Diana-microT | Dynamic programming - dinucleotides | Hybridisation energy < -20 kcal/mole + other rules must be fulfilled about the complete alignment | No | Modifyable energy cutoff + hard rules | No | Yes | No |
| MicroInspector | Perfect seed, followed by alignment | Hybridization energy from Vienna RNA | None implemented | Sort by energy | No | Yes | No |
| miTarget | Short seed | hard cutoff (adjustable) | None implemented | SVM that weight a combination of features learned from examples | No | Yes | No |
Gene prediction
This is an expanded version of the table appearing in our review-paper. This table also includes publications, where the method used is unnamed and not generally available.
| Name | Method | Description | Applied to | Downloadable program | Webserver | Database with results | Reference | Year |
|---|---|---|---|---|---|---|---|---|
| MirScan | Hybrid: Rule based and using empirical values of parameters | RNAfold hairpins compared between organisms | Worm, human, mouse, pufferfish | - | Yes | PMID:12624257 | 2003 | |
| "no name given" | Filtering C. elegans hairpins and search for conservation to other worms and Drosophila and Human | C. elegans | PMID:12769849 | 2003 | ||||
| "no name given" | PMID:12796779 | 2003 | ||||||
| "no name given" | Comparative genomics including mfold predicted hairpins. | C. elegans | PMID:12747828 | 2003 | ||||
| "no name given" | Detection of upstream conserved motif of miRNAs | Worm | PMID:15317971 | 2004 | ||||
| "no name given" | Genomic location of miRNAs | Human and mouse | PMID:15364901 | 2004 | ||||
| MIRFINDER | Use comparative genomics and structural homology | Rice and Arabidopsis | Yes | - | Yes | PMID:15272084 | 2004 | |
| "no name given" | Hairpins and sequence conservation. | Arabidopsis and rice | PMID:15345049 | 2004 | ||||
| "no name given" | Search simulataneous for microRNA and targets. Organisms specific. | Arabidopsis | PMID:15200956 | 2004 | ||||
| "no name given" | Conserved genomic regions of miRNAs (Phylogenetic shadowing) | Mammalian genomes | PMID:15652478 | 2005 | ||||
| PalGrade | Filtering RNAfold predicted hairpins | Human and primate genomes | - | - | - | PMID:15965474 | 2005 | |
| ProMiR | Genetic programming. Learning pre-miRNA features. | Human conservation to vertebrates | - | Yes | Yes | PMID:15987789 | 2005 | |
| "no name given" | Search for miRNA clusters | human, mouse, rat and virus | PMID:15782219 | 2005 | ||||
| "no name given" | General approach to search for regulatory motifs in promotors and 3'UTR. | Human mouse rat dog | PMID:15735639 | 2005 | ||||
| "no name given" | Homology search of both pre-miRNA and mature miRNA | Human and mouse | PMID:15634332 | 2005 | ||||
| ERPIN to construct profiles | Profiles search to for | Animal genomes | PMID:15509608 | 2005 | ||||
| findMiRNA | miRNA patterns from training set | Arabidopsis and Rice | - | - | Yes | PMID:15632092 | 2005 | |
| "no name given" | Using EST to find siRNA [DO they really find microRNAs?] | Arabidopsis | PMID:15980147 | 2005 | ||||
| Triplet-SVM | SVM | Approach to distingush between real pre-miRNA hairpins from others. | Human applied on plant and virus. | Yes | - | - | PMID:16381612 | 2005 |
| BayesmiRNAfind | "Naiive Bayes" | As mirScan fold 110 nt genomic sequences then apply a bayes filter trained on XXX | worm, vertebrate, plant and virus | - | Yes | - | PMID:16543277 | 2006 |
| microHARVESTER | Find miRNAs homolog to existing ones. BLAST then structural filters. | Plants | - | Yes | - | PMID:16317073 | 2006 | |
| RNAmicro | SVM | Use multiple alignments to predict microRNA hairpins | Mammals, urochordates, and nematodes. | Yes | Yes | - | PMID:16873472 | 2006 |
| miMatcher | SVM | Intragenomic matching to simultaneously find miRNAs and their targets | arabidopsis, rice, poplar | - | - | Yes | PMID:16159385 | 2006 |
Useful databases
- miRBase - 'Official' tracker of miRNA-genes
- RFAM - Database of RNA families and covariance models describing them.
- miRNAmap - Alternative interface to miRBase + some of their own predictions and expression data
- Tarbase - Compilation of some experimentally validated miRNA-target interactions
General software for searching for ncRNA
