Help contents

Overview of Transterm

Transterm is an interactive database providing access to RNA sequences, their associated motifs and search tools.

The RNA sequences are derived from all gene sequence data from NCBI complete genomes and Genbank. Only species with 40 or more CDS are processed

The mRNA or genomic sequence data are divided into five regions: putative 5' and 3' UTRs, initiation and termination regions and the full CDS sequences. These data can be searched for motifs or you can obtain summaries about each type of sequence region for each species in Genbank for a range of properties including codon usage, RSCU values, information content, etc.

Using the Transterm website

The first form allows you to select a species and data type to examine using the buttons immediately below it.

The second form allows you to search the RNA regions for the species selected using the available patterns, or a pattern of your choosing. A more detailed description of using Transterm is found in later sections of this help a short form here.

To alter the species, first choose a database (default human genomic, nuclear genes).

Next you will need to enter a taxon. The NCBI taxonomy database assigns one taxon to each species or strain present in Genbank.

On entering a new taxon, the species name Homo sapiens, to the right of the "clear Taxon" button, will be replaced with Click to show species selected. If you want to confirm what your taxon represents, click on the text Click to show species selected and the organism name will be shown.

Next select one of the common data files available.The size of the data file will be presented below the "Preview and email" and "Download" buttons.

Preview the first 300 lines of the file or download the file.

To search the sequence regions, select the species, then select a sequence region. Next choose to search non-redundant sequence data (i.e. duplicates removed) or all the sequences.

Either choose a pre-defined pattern to use or enter your own pattern. Search and a window will open to enter your email and the results will be sent to you.

You can also view the description of pattern, which includes details on where it is located, literature references and so on.

Transterm requires that Javascript be active in your browser: this is usually the case by default, but if some of the buttons appear not to be responding, this will be the most likely cause.

Contact us

The home page for bioinformatics resources (Brown Group) at the University of Otago can be found at the Bioinformatics and Computational Molecular Biology page of the Department of Biochemistry.

Transterm was developed with the assistance of a computational biology consultant, Dr. Grant Jacobs of BioinfoTools.

Citing Transterm

If you use Transterm for your work, please cite your use of Transterm.

General use e.g. stops, regulatory RNA signals

Transterm: a database of messenger RNA components and signals (2000) GH Jacobs, PA Stockwell, MJ Schrieber, WP Tate, CM Brown Nucleic acids research 28 (1), 293-295

Use of initiation contexts or codon usage

The translational termination signal database (TransTerm) now also includes initiation contexts (1994) CM Brown, PA Stockwell, ME Dalphin, WP Tate Nucleic acids research 22 (17), 3620-3624