Marco, Antonio (2018) SeedVicious: Analysis of microRNA target and near-target sites. PLoS ONE, 13 (4). e0195532-e0195532. DOI https://doi.org/10.1371/journal.pone.0195532
Marco, Antonio (2018) SeedVicious: Analysis of microRNA target and near-target sites. PLoS ONE, 13 (4). e0195532-e0195532. DOI https://doi.org/10.1371/journal.pone.0195532
Marco, Antonio (2018) SeedVicious: Analysis of microRNA target and near-target sites. PLoS ONE, 13 (4). e0195532-e0195532. DOI https://doi.org/10.1371/journal.pone.0195532
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.
Item Type: | Article |
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Uncontrolled Keywords: | Humans; MicroRNAs; RNA, Messenger; Computational Biology; Gene Expression Regulation; Algorithms; Software; User-Computer Interface |
Subjects: | Q Science > QH Natural history > QH301 Biology |
Divisions: | Faculty of Science and Health Faculty of Science and Health > Life Sciences, School of |
SWORD Depositor: | Unnamed user with email elements@essex.ac.uk |
Depositing User: | Unnamed user with email elements@essex.ac.uk |
Date Deposited: | 30 Apr 2018 09:23 |
Last Modified: | 07 Aug 2024 20:27 |
URI: | http://repository.essex.ac.uk/id/eprint/21914 |
Available files
Filename: journal.pone.0195532.pdf
Licence: Creative Commons: Attribution 3.0