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Transterm


NAR Molecular Biology Database Collection entry number 48
Jacobs, G.2, Rackham, O.1, Stockwell, P. A.1, Brown, C. M.1
1Biochemistry Department and Centre for Gene Research University of Otago PO Box 56 Dunedin New Zealand
2Bioinfotools PO Box 6129 Dunedin New Zealand

Database Description

Transterm is a database that facilitates studies of translation and the translational control of protein synthesis. It contains a curated collection of motifs in mRNAs that control translation, and also biologically relevant mRNA regions extracted from GenBank. It is organised largely on a taxonomic basis with files and summaries for each species. Global patterns that may affect translation in particular species for example bias in the context of initiation codons (Kozaks consensus, or Shine Dalgarno sequences) or termination codons can be detected in the summary consensus and information content biases summaries. Several types of access are provided via a web browser interface. Transterm defined motifs may be matched in a users sequence or in the database. Alternatively, motifs can be entered by the user to search specific sections of the database (for example coding regions or 3' flanking regions) or the user's sequence. Each Transterm defined motif has an associated biological description with references. The database is accessible at http://uther.otago.ac.nz/Transterm.html

Recent Developments

The web interface has been revised to allow users to analyse their own sequences. All motifs description have been revised, new specific patterns have been added. Transterm data was updated with Genbank 122 (Feb 2001).

Acknowledgements

Health Research Council of New Zealand Marsden Fund of New Zealand


Go to the abstract in the NAR 2009 Database Issue.
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