TransTerm, the translational signal database, extended to include full coding sequences and untranslated regions

Abstract

TransTerm is a database of mRNA sequences and parameters useful for detecting translational control signals in general. TransTerm-98 has been expanded beyond previous years to include full coding sequences and UTRs, while retaining the original small contexts about the coding sequence start- and stop-codons. The database contains more than 130,000 non-redundant coding sequences with associated untranslated regions (UTRs) from over 450 species. This includes the complete genomes of 12 prokaryotic and one eukaryotic organism. Several coding sequence parameters are available: coding sequence length, Nc, GC3 and, when it is computable, Codon Adaptation Index (CAI). Codon usage tables and summaries of start- and stop-codon contexts are also included. TransTerm-98 has both a relational database form with a WWW interface and a flatfile format, also available by Internet browser. TransTerm is available at: http://biochem.otago.ac.nz:800/Transterm/homepage.html.