title: DETECTION OF BACTERIAL SMALL TRANSCRIPTS FROM RNA-SEQ DATA: A COMPARATIVE ASSESSMENT.
abstract: Small non-coding RNAs (sRNAs) are regulatory RNA molecules that have been identified in a multitude of bacterial species and shown to control numerous cellular processes through various regulatory mechanisms. In the last decade, next generation RNA sequencing (RNA-seq) has been used for the genome-wide detection of bacterial sRNAs. Here we describe sRNA-Detect, a novel approach to identify expressed small transcripts from prokaryotic RNA-seq data. Using RNA-seq data from three bacterial species and two sequencing platforms, we performed a comparative assessment of five computational approaches for the detection of small transcripts. We demonstrate that sRNA-Detect improves upon current standalone computational approaches for identifying novel small transcripts in bacteria.
authors.affiliation: Department of Computer Science, Memorial University of Newfoundland, St. John's, NL, Canada2Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada, lourdes@mun.ca.
authors.forename: Lourdes
authors.initials: L
authors.lastname: Peña-Castillo
authors.forename: Marc
authors.initials: M
authors.lastname: Grüell
authors.forename: Martin E
authors.initials: ME
authors.lastname: Mulligan
authors.forename: Andrew S
authors.initials: AS
authors.lastname: Lang
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D030561:Databases, Nucleic Acid / Q000706:statistics & numerical data; D034301:Deinococcus / Q000235:genetics; D044084:Erwinia amylovora / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000706:statistics & numerical data*; D008390:Markov Chains; D012329:RNA, Bacterial / Q000235:genetics*; D058727:RNA, Small Untranslated / Q000235:genetics*; D016354:Rhodobacter capsulatus / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000706:statistics & numerical data*; D012984:Software; D012985:Software Design
chemical_list: D012329:RNA, Bacterial; D058727:RNA, Small Untranslated