Please use this identifier to cite or link to this item: https://hdl.handle.net/11147/5289
Title: Comparison of four Ab initio MicroRNA prediction tools
Authors: Saçar, Müşerref Duygu
Allmer, Jens
Saçar, Müşerref Duygu
Allmer, Jens
Izmir Institute of Technology. Molecular Biology and Genetics
Keywords: Ab initio
RNA
MiRNA
Comparison
Bioinformatics
Issue Date: 2013
Publisher: SciTePress
Source: Saçar, M. D., and Allmer, J. (2013). Comparison of four Ab initio MicroRNA prediction tools. In P. Fernandes (Ed.). Paper presented at the BIOINFORMATICS 2013 proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Barcelona, Spain, 11-14 February (pp. 190-195). Setúbal, Portugal: SciTePress.
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. Copyright © 2013 SCITEPRESS - Science and Technology Publications.
Description: International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2013; Barcelona; Spain; 11 February 2013 through 14 February 2013
URI: http://hdl.handle.net/11147/5289
ISBN: 9789898565358
Appears in Collections:Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection

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