title: GWIPS-viz: development of a ribo-seq genome browser.
abstract: We describe the development of GWIPS-viz (http://gwips.ucc.ie), an online genome browser for viewing ribosome profiling data. Ribosome profiling (ribo-seq) is a recently developed technique that provides genome-wide information on protein synthesis (GWIPS) in vivo. It is based on the deep sequencing of ribosome-protected messenger RNA (mRNA) fragments, which allows the ribosome density along all mRNA transcripts present in the cell to be quantified. Since its inception, ribo-seq has been carried out in a number of eukaryotic and prokaryotic organisms. Owing to the increasing interest in ribo-seq, there is a pertinent demand for a dedicated ribo-seq genome browser. GWIPS-viz is based on The University of California Santa Cruz (UCSC) Genome Browser. Ribo-seq tracks, coupled with mRNA-seq tracks, are currently available for several genomes: human, mouse, zebrafish, nematode, yeast, bacteria (Escherichia coli K12, Bacillus subtilis), human cytomegalovirus and bacteriophage lambda. Our objective is to continue incorporating published ribo-seq data sets so that the wider community can readily view ribosome profiling information from multiple studies without the need to carry out computational processing.
authors.affiliation: School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland, School of Medicine & Medical Science, Conway Institute, University College Dublin, Dublin 4, Ireland and Howest, University College West Flanders, Rijselstraat 5, 8200 Bruges, Belgium.
authors.forename: Audrey M
authors.initials: AM
authors.lastname: Michel
authors.forename: Gearoid
authors.initials: G
authors.lastname: Fox
authors.forename: Anmol
authors.initials: A
authors.lastname: M Kiran
authors.forename: Christof
authors.initials: C
authors.lastname: De Bo
authors.forename: Patrick B F
authors.initials: PB
authors.lastname: O'Connor
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Heaphy
authors.forename: James P A
authors.initials: JP
authors.lastname: Mullan
authors.forename: Claire A
authors.initials: CA
authors.lastname: Donohue
authors.forename: Desmond G
authors.initials: DG
authors.lastname: Higgins
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Baranov
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020407:Internet; D051379:Mice; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000737:chemistry; D012270:Ribosomes / Q000378:metabolism; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D064878:Web Browser
chemical_list: D012333:RNA, Messenger