Transterm: a database of messenger RNA components and signals
Open Access
- 1 January 2000
- journal article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 28 (1) , 293-295
- https://doi.org/10.1093/nar/28.1.293
Abstract
Transterm facilitates studies of messenger RNAs and translational control signals. Each messenger RNA (mRNA) from GenBank is extracted and broken into its functional components, its coding sequence, initiation context, termination context, flanking sequence representing its 5′ UTR (untranslated region), 3′ UTR and translational signals. In addition, numerical parameters characterising each coding region in Transterm, including codon and GC bias, are available. For each species in Transterm, the initiation and termination regions are aligned by their start or stop codons and presented as base frequency matrices and tables of the information content of the bases in the alignments. Users can obtain summaries of characteristics of the mRNAs for species of their choice and search for translational signals both in the Transterm database and in their own sequence. The current release contains data from over 10 000 species, including the complete genomes of 20 prokaryotes and three eukaryotes. Both flat-file and relational database forms of Transterm are accessible via the WWW at http://biochem.otago. ac.nz/Transterm/Keywords
This publication has 12 references indexed in Scilit:
- TransTerm, the translational signal database, extended to include full coding sequences and untranslated regionsNucleic Acids Research, 1999
- Linking up with entrezTrends in Genetics, 1998
- Displaying the in formation contents of structural RNA alignments: the structure logosBioinformatics, 1997
- CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databasesBioinformatics, 1996
- The translational termination signal databaseNucleic Acids Research, 1993
- The ‘effective number of codons’ used in a geneGene, 1990
- The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applicationsNucleic Acids Research, 1987
- Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomesCell, 1986
- A comprehensive set of sequence analysis programs for the VAXNucleic Acids Research, 1984
- The 3′-Terminal Sequence of Escherichia coli 16S Ribosomal RNA: Complementarity to Nonsense Triplets and Ribosome Binding SitesProceedings of the National Academy of Sciences, 1974