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  • Small Open Reading Frames: Current Prediction Techniques and Future Prospect

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    Author(s)
    Cheng, Haoyu
    Chan, Wai Soon
    Li, Zhixiu
    Wang, Dan
    Liu, Song
    Zhou, Yaoqi
    Griffith University Author(s)
    Zhou, Yaoqi
    Year published
    2011
    Metadata
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    Abstract
    Evidence is accumulating that small open reading frames (sORF, <100 codons) play key roles in many important biological processes. Yet, they are generally ignored in gene annotation despite they are far more abundant than the genes with more than 100 codons. Here, we demonstrate that popular homolog search and codon-index techniques perform poorly for small genes relative to that for larger genes, while a method dedicated to sORF discovery has a similar level of accuracy as homology search. The result is largely due to the small dataset of experimentally verified sORF available for homology search and for training ab initio ...
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    Evidence is accumulating that small open reading frames (sORF, <100 codons) play key roles in many important biological processes. Yet, they are generally ignored in gene annotation despite they are far more abundant than the genes with more than 100 codons. Here, we demonstrate that popular homolog search and codon-index techniques perform poorly for small genes relative to that for larger genes, while a method dedicated to sORF discovery has a similar level of accuracy as homology search. The result is largely due to the small dataset of experimentally verified sORF available for homology search and for training ab initio techniques. It highlights the urgent need for both experimental and computational studies in order to further advance the accuracy of sORF prediction.
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    Journal Title
    Current Protein and Peptide Science
    Volume
    12
    Issue
    6
    DOI
    https://doi.org/10.2174/138920311796957667
    Copyright Statement
    © 2011 Bentham Science Publishers. This is the author-manuscript version of this paper. Reproduced in accordance with the copyright policy of the publisher. Please refer to the journal website for access to the definitive, published version.
    Subject
    Medicinal and biomolecular chemistry
    Physical chemistry
    Biochemistry and cell biology
    Publication URI
    http://hdl.handle.net/10072/57456
    Collection
    • Journal articles

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