title: Transterm: a database to aid the analysis of regulatory sequences in mRNAs.
abstract: Messenger RNAs, in addition to coding for proteins, may contain regulatory elements that affect how the protein is translated. These include protein and microRNA-binding sites. Transterm (http://mRNA.otago.ac.nz/Transterm.html) is a database of regions and elements that affect translation with two major unique components. The first is integrated results of analysis of general features that affect translation (initiation, elongation, termination) for species or strains in Genbank, processed through a standard pipeline. The second is curated descriptions of experimentally determined regulatory elements that function as translational control elements in mRNAs. Transterm focuses on protein binding sites, particularly those in 3'-untranslated regions (3'-UTR). For this release the interface has been extensively updated based on user feedback. The data is now accessible by strain rather than species, for example there are 10 Escherichia coli strains (genomes) analysed separately. In addition to providing a repository of data, the database also provides tools for users to query their own mRNA sequences. Users can search sequences for Transterm or user defined regulatory elements, including protein or miRNA targets. Transterm also provides a central core of links to related resources for complementary analyses.
authors.affiliation: Biochemistry Department and Webster Centre, University of Otago, PO Box 56 and Bioinfotools, PO Box 6129, Dunedin, New Zealand.
authors.forename: Grant H
authors.initials: GH
authors.lastname: Jacobs
authors.forename: Augustine
authors.initials: A
authors.lastname: Chen
authors.forename: Stewart G
authors.initials: SG
authors.lastname: Stevens
authors.forename: Peter A
authors.initials: PA
authors.lastname: Stockwell
authors.forename: Michael A
authors.initials: MA
authors.lastname: Black
authors.forename: Warren P
authors.initials: WP
authors.lastname: Tate
authors.forename: Chris M
authors.initials: CM
authors.lastname: Brown
mesh_terms: D030561:Databases, Nucleic Acid; D014176:Protein Biosynthesis; D012329:RNA, Bacterial / Q000737:chemistry; D012333:RNA, Messenger / Q000737:chemistry*; D038621:Regulatory Sequences, Ribonucleic Acid; D017423:Sequence Analysis, RNA
chemical_list: D012329:RNA, Bacterial; D012333:RNA, Messenger; D038621:Regulatory Sequences, Ribonucleic Acid