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Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik

Permanent URI for this collectionhttps://hdl.handle.net/11147/9

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Browsing Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik by Subject "Ab initio"

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    Citation - WoS: 6
    Citation - Scopus: 8
    Comparison of Four Ab Initio Microrna Prediction Tools
    (SciTePress, 2013) Saçar, Müşerref Duygu; Allmer, Jens; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    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.
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    Citation - Scopus: 29
    Computational Methods for Ab Initio Detection of Micrornas
    (Frontiers Media S.A., 2012) Allmer, Jens; Yousef, Malik; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    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 via the microprocessor complex, yielding a hairpin structure. Which is then exported into the cytosol where it is processed by Dicer and then incorporated into the RNA-induced silencing complex. All of these biogenesis steps add to the overall specificity of miRNA production and effect. Unfortunately, their modes of action are just beginning to be elucidated and therefore computational prediction algorithms cannot model the process but are usually forced to employ machine learning approaches. This work focuses on ab initio prediction methods throughout; and therefore homology-based miRNA detection methods are not discussed. Current ab initio prediction algorithms, their ties to data mining, and their prediction accuracy are detailed.