» Articles » PMID: 29664927

SeedVicious: Analysis of MicroRNA Target and Near-target Sites

Overview
Journal PLoS One
Date 2018 Apr 18
PMID 29664927
Citations 13
Authors
Affiliations
Soon will be listed here.
Abstract

Here I describe seedVicious, a versatile microRNA target site prediction software that can be easily fitted into annotation pipelines and run over custom datasets. SeedVicious finds microRNA canonical sites plus other, less efficient, target sites. Among other novel features, seedVicious can compute evolutionary gains/losses of target sites using maximum parsimony, and also detect near-target sites, which have one nucleotide different from a canonical site. Near-target sites are important to study population variation in microRNA regulation. Some analyses suggest that near-target sites may also be functional sites, although there is no conclusive evidence for that, and they may actually be target alleles segregating in a population. SeedVicious does not aim to outperform but to complement existing microRNA prediction tools. For instance, the precision of TargetScan is almost doubled (from 11% to ~20%) when we filter predictions by the distance between target sites using this program. Interestingly, two adjacent canonical target sites are more likely to be present in bona fide target transcripts than pairs of target sites at slightly longer distances. The software is written in Perl and runs on 64-bit Unix computers (Linux and MacOS X). Users with no computing experience can also run the program in a dedicated web-server by uploading custom data, or browse pre-computed predictions. SeedVicious and its associated web-server and database (SeedBank) are distributed under the GPL/GNU license.

Citing Articles

High-throughput microRNA sequencing in the developing branchial arches suggests miR-92b-3p regulation of a cardiovascular gene network.

Goldsworthy S, Losa M, Bobola N, Griffiths-Jones S Front Genet. 2025; 16:1514925.

PMID: 40051700 PMC: 11882518. DOI: 10.3389/fgene.2025.1514925.


Predictive modeling of oocyte maternal mRNA features for five mammalian species reveals potential shared and species-restricted regulators during maturation.

Schall P, Latham K Physiol Genomics. 2023; 56(1):9-31.

PMID: 37842744 PMC: 11281819. DOI: 10.1152/physiolgenomics.00048.2023.


Exon-intron split analysis reveals posttranscriptional regulatory signals induced by high and low n-6/n-3 polyunsaturated fatty acid ratio diets in piglets.

Manaig Y, Marmol-Sanchez E, Castello A, Esteve-Codina A, Sandrini S, Savoini G J Anim Sci. 2023; 101.

PMID: 37561402 PMC: 10503648. DOI: 10.1093/jas/skad271.


Resources and Methods for the Analysis of MicroRNA Function in Drosophila.

Mukherjee S, Sokol N Methods Mol Biol. 2022; 2540:79-92.

PMID: 35980573 DOI: 10.1007/978-1-0716-2541-5_3.


Urinary microRNAome in healthy cats and cats with pyelonephritis or other urological conditions.

Godia M, Brogaard L, Marmol-Sanchez E, Langhorn R, Kieler I, Jan Reezigt B PLoS One. 2022; 17(7):e0270067.

PMID: 35857780 PMC: 9299306. DOI: 10.1371/journal.pone.0270067.


References
1.
Saunders M, Liang H, Li W . Human polymorphism at microRNAs and microRNA target sites. Proc Natl Acad Sci U S A. 2007; 104(9):3300-5. PMC: 1805605. DOI: 10.1073/pnas.0611347104. View

2.
He L, Hannon G . MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet. 2004; 5(7):522-31. DOI: 10.1038/nrg1379. View

3.
Denzler R, McGeary S, Title A, Agarwal V, Bartel D, Stoffel M . Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression. Mol Cell. 2016; 64(3):565-579. PMC: 5101187. DOI: 10.1016/j.molcel.2016.09.027. View

4.
Marco A . Selection Against Maternal microRNA Target Sites in Maternal Transcripts. G3 (Bethesda). 2015; 5(10):2199-207. PMC: 4593001. DOI: 10.1534/g3.115.019497. View

5.
Maragkakis M, Alexiou P, Papadopoulos G, Reczko M, Dalamagas T, Giannopoulos G . Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics. 2009; 10:295. PMC: 2752464. DOI: 10.1186/1471-2105-10-295. View