title: SeqTU: A Web Server for Identification of Bacterial Transcription Units.
abstract: A transcription unit (TU) consists of K ≥ 1consecutive genes on the same strand of a bacterial genome that are transcribed into a single mRNA molecule under certain conditions. Their identification is an essential step in elucidation of transcriptional regulatory networks. We have recently developed a machine-learning method to accurately identify TUs from RNA-seq data, based on two features of the assembled RNA reads: the continuity and stability of RNA-seq coverage across a genomic region. While good performance was achieved by the method on Escherichia coli and Clostridium thermocellum, substantial work is needed to make the program generally applicable to all bacteria, knowing that the program requires organism specific information. A web server, named SeqTU, was developed to automatically identify TUs with given RNA-seq data of any bacterium using a machine-learning approach. The server consists of a number of utility tools, in addition to TU identification, such as data preparation, data quality check and RNA-read mapping. SeqTU provides a user-friendly interface and automated prediction of TUs from given RNA-seq data. The predicted TUs are displayed intuitively using HTML format along with a graphic visualization of the prediction.
authors.affiliation: College of Computer Science and Technology, Jilin University, Changchun, Jilin, China.|Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, GA, USA.|BioEnergy Science Center, USA.|Center for Applied Mathematics, Tianjin University, Tianjin, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Chen
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Wen-Chi
authors.initials: WC
authors.lastname: Chou
authors.affiliation: Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA.|BioSNTR, Brookings, SD, USA.
authors.forename: Qin
authors.initials: Q
authors.lastname: Ma
authors.affiliation: College of Computer Science and Technology, Jilin University, Changchun, Jilin, China.|Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, GA, USA.|BioEnergy Science Center, USA.
authors.forename: Ying
authors.initials: Y
authors.lastname: Xu
mesh_terms: D001419:Bacteria / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D020407:Internet; D000069550:Machine Learning; D017423:Sequence Analysis, RNA; D012984:Software; D014158:Transcription, Genetic