title: TIPR: transcription initiation pattern recognition on a genome scale.
abstract: BACKGROUND
  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.
  
  
  METHODS
  Model source code is made available online at http://megraw.cgrb.oregonstate.edu/software/TIPR/.
  
  
  BACKGROUND
  megrawm@science.oregonstate.edu.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA.
authors.forename: Taj
authors.initials: T
authors.lastname: Morton
authors.affiliation: Department of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA.
authors.forename: Weng-Keen
authors.initials: WK
authors.lastname: Wong
authors.affiliation: Department of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.
authors.forename: Molly
authors.initials: M
authors.lastname: Megraw
mesh_terms: D000465:Algorithms; D023281:Genomics; D000069550:Machine Learning; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA; D012984:Software; D024363:Transcription Initiation Site; D061785:Transcription Initiation, Genetic