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TIPR: Transcription Initiation Pattern Recognition on a Genome Scale

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https://ir.library.oregonstate.edu/concern/articles/vd66w186d

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  • MOTIVATION: The computational identification of gene transcription start sites (TSSs) can provide insights into the regulation and function of genes without performing expensive experiments, particularly in organisms with incomplete annotations. High-resolution general-purpose TSS prediction remains a challenging problem, with little recent progress on the identification and differentiation of TSSs which are arranged in different spatial patterns along the chromosome. RESULTS: In this work, we present the Transcription Initiation Pattern Recognizer (TIPR), a sequence-based machine learning model that identifies TSSs with high accuracy and resolution for multiple spatial distribution patterns along the genome, including broadly distributed TSS patterns that have previously been difficult to characterize. TIPR predicts not only the locations of TSSs but also the expected spatial initiation pattern each TSS will form along the chromosome—a novel capability for TSS prediction algorithms. As spatial initiation patterns are associated with spatiotemporal expression patterns and gene function, this capability has the potential to improve gene annotations and our understanding of the regulation of transcription initiation. The high nucleotide resolution of this model locates TSSs within 10 nucleotides or less on average. AVAILABILITY AND IMPLEMENTATION: Model source code is made available online at http://megraw.cgrb.oregonstate.edu/software/TIPR/.
  • This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the author(s) and published by Oxford University Press. It can be found at: http://bioinformatics.oxfordjournals.org/,Supplementary information: Supplementary data are available at Bioinformatics online. Availability and implementation: Model source code is made available online at http://megraw.cgrb.oregonstate.edu/software/TIPR/.
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  • Morton, T., Wong, W. K., & Megraw, M. (2015). TIPR: transcription initiation pattern recognition on a genome scale. Bioinformatics, 31(23), 3725-3732. doi:10.1093/bioinformatics/btv464
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  • 31
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  • 23
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  • This work was supported by the National Institutes of Health [GM097188 to M.M]; and by startup funds from Oregon State University.
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