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Nucleic Acids Research Advance Access originally published online on November 4, 2008
Nucleic Acids Research 2009 37(Database issue):D72-D76; doi:10.1093/nar/gkn763
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Nucleic Acids Research, 2009, Vol. 37, Database issue D72-D76
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

Transterm: a database to aid the analysis of regulatory sequences in mRNAs

Grant H. Jacobs1,2, Augustine Chen1, Stewart G. Stevens1, Peter A. Stockwell1, Michael A. Black1, Warren P. Tate1 and Chris M. Brown1,*

1Biochemistry Department and Webster Centre, University of Otago, PO Box 56 and 2Bioinfotools, PO Box 6129, Dunedin, New Zealand

*To whom correspondence should be addressed. Tel: +643 4795201; Fax: +643 4797866; Email: chris.brown{at}otago.ac.nz

Received September 16, 2008. Revised October 6, 2008. Accepted October 6, 2008.

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.


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