title: Detection of signals in mRNAs that influence translation.
abstract: Genome sequencing efforts mean that we now have extensive data from a wide range of organisms to study. Understanding the differing natures of the biology of these organisms is an important aim of genome analysis. We are interested in signals that affect translation of mRNAs. Some signals in the mRNA influence how efficiently it is translated into protein. Previous studies have indicated that many important signals are located around the initiation and termination codons. We have developed tools described here to extract the relevant sequence regions from GenBank. To create databases organised by species, or higher taxonomic groupings (eg planta), a program was developed to dynamically view and edit the taxonomy database. Data from relevant species were then extracted using our Genbank feature table parser. We analysed all available sequences, particularly those from complete genomes. Patterns were then identified using information theory. The software is available from http://transterm.otago.ac.nz. Patterns around the initiation codons for most of the organisms fall into two groups, containing the previously known Shine-Dalgarno and Kozaks efficiency signals. However, we have identified several organisms that appear to utilise novel systems. Our analysis indicates that some organisms with extremely high GC% genomes do not have a strong dependence on base pairing ribosome binding sites, as the complementary sequence is absent from many genes.
authors.affiliation: Biochemistry Department, University of Otago, Dunedin, New Zealand. chris.brown@otago.ac.nz
authors.forename: Chris M
authors.initials: CM
authors.lastname: Brown
authors.forename: Grant
authors.initials: G
authors.lastname: Jacobs
authors.forename: Peter
authors.initials: P
authors.lastname: Stockwell
authors.forename: Mark
authors.initials: M
authors.lastname: Schreiber
mesh_terms: D000043:Abstracting and Indexing / Q000379:methods*; D000465:Algorithms; D001483:Base Sequence; D030561:Databases, Nucleic Acid; D004282:Documentation / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods; D008969:Molecular Sequence Data; D014176:Protein Biosynthesis / Q000235:genetics*; D012313:RNA / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D013045:Species Specificity; D009626:Terminology as Topic
chemical_list: D012313:RNA