Comparison of Four Ab Initio MicroRNA Prediction Tools

Müşerref Duygu Saçar, Jens Allmer

Abstract

MicroRNAs are small RNA sequences of 18-24 nucleotides in length, which serve as templates to drive post transcriptional gene silencing. The canonical microRNA pathway starts with transcription from DNA and is followed by processing by the Microprocessor complex, yielding a hairpin structure. This is then exported into the cytosol where it is processed by Dicer and next incorporated into the RNA induced silencing complex. All of these biogenesis steps add to the overall specificity of miRNA production and effect. Unfortunately, experimental detection of miRNAs is cumbersome and therefore computational tools are necessary. Homology-based miRNA prediction tools are limited by fast miRNA evolution and by the fact that they are template driven. Ab initio miRNA prediction methods have been proposed but they have not been analyzed competitively so that their relative performance is largely unknown. Here we implement the features proposed in four miRNA ab initio studies and evaluate them on two data sets. Using the features described in Bentwich 2008 leads to the highest accuracy but still does not provide enough confidence into the results to warrant experimental validation of all predictions in a larger genome like the human genome.

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Paper Citation


in Harvard Style

Saçar M. and Allmer J. (2013). Comparison of Four Ab Initio MicroRNA Prediction Tools . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013) ISBN 978-989-8565-35-8, pages 190-195. DOI: 10.5220/0004248201900195


in Bibtex Style

@conference{bioinformatics13,
author={Müşerref Duygu Saçar and Jens Allmer},
title={Comparison of Four Ab Initio MicroRNA Prediction Tools},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)},
year={2013},
pages={190-195},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004248201900195},
isbn={978-989-8565-35-8},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)
TI - Comparison of Four Ab Initio MicroRNA Prediction Tools
SN - 978-989-8565-35-8
AU - Saçar M.
AU - Allmer J.
PY - 2013
SP - 190
EP - 195
DO - 10.5220/0004248201900195