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Nucleic Acids Research, 2003, Vol. 31, No. 1 446-447
© 2003 Oxford University Press

tmRDB (tmRNA database)

Christian Zwieb*, Jan Gorodkin1, Bjarne Knudsen2, Jody Burks and Jacek Wower3

Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler, TX 75708-3154, USA 1 Division of Genetics, The Royal Veterinary and Agricultural University, Institute of Animal Science and Animal Health, Groennegaardsvej 3, DK-1870 Frederiksberg C, Denmark 2 Bioinformatics Research Center, University of Aarhus, Høegh Guldbergsgade 10, DK-8000 Aarhus C, Denmark 3 Department of Animal and Dairy Sciences, Program in Cellular and Molecular Biosciences, Auburn University, Auburn, AL 36849-5415, USA

*To whom correspondence should be addressed. Tel: +1 903 877 7689; Fax: +1 903 877 5731; Email: zwieb{at}uthct.edu

ABSTRACT

Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html with mirror sites located at Auburn University, Auburn, Alabama (http://www.ag.auburn.edu/mirror/tmRDB/) and the Bioinformatics Research Center, Aarhus, Denmark (http://www.bioinf.au.dk/tmRDB/). The tmRDB collects and distributes information relevant to the study of tmRNA. In trans-translation, this molecule combines properties of tRNA and mRNA and binds several proteins to form the tmRNP. Related RNPs are likely to be functional in all bacteria. In this release of tmRDB, 186 new entries from 10 bacterial groups for a total of 274 tmRNA sequences have been added. Lists of the tmRNAs and the corresponding tmRNA-encoded tag-peptides are presented in alphabetical and phylogenetic order. The tmRNA sequences are aligned manually, assisted by computational tools, to determine base pairs supported by comparative sequence analysis. The tmRNA alignment, available in a variety of formats, provides the basis for the secondary and tertiary structure of each tmRNA molecule. Three-dimensional models of the tmRNAs and their associated proteins in PDB format give evidence for the recent progress that has been made in the understanding of tmRNP structure and function.


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