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Nucleic Acids Research 2006 34(Database Issue):D37-D40; doi:10.1093/nar/gkj159
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Nucleic Acids Research, 2006, Vol. 34, Database issue D37-D40
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Transterm—extended search facilities and improved integration with other databases

Grant H. Jacobs1, Peter A. Stockwell, Warren P. Tate and Chris M. Brown*

Department of Biochemistry and Centre for Gene Research, University of Otago PO Box 56, Dunedin, New Zealand 1Bioinfotools PO Box 6129, Dunedin, New Zealand

*To whom correspondence should be addressed. Email: chris.brown{at}otago.ac.nz

Received September 16, 2005. Revised October 31, 2005. Accepted October 31, 2005.

Transterm has now been publicly available for >10 years. Major changes have been made since its last description in this database issue in 2002. The current database provides data for key regions of mRNA sequences, a curated database of mRNA motifs and tools to allow users to investigate their own motifs or mRNA sequences. The key mRNA regions database is derived computationally from Genbank. It contains 3' and 5' flanking regions, the initiation and termination signal context and coding sequence for annotated CDS features from Genbank and RefSeq. The database is non-redundant, enabling summary files and statistics to be prepared for each species. Advances include providing extended search facilities, the database may now be searched by BLAST in addition to regular expressions (patterns) allowing users to search for motifs such as known miRNA sequences, and the inclusion of RefSeq data. The database contains >40 motifs or structural patterns important for translational control. In this release, patterns from UTRsite and Rfam are also incorporated with cross-referencing. Users may search their sequence data with Transterm or user-defined patterns. The system is accessible at http://uther.otago.ac.nz/Transterm.html.


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