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Nucleic Acids Research 2006 34(Database Issue):D163-D168; doi:10.1093/nar/gkj142
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Nucleic Acids Research, 2006, Vol. 34, Database issue D163-D168
© 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

The tmRDB and SRPDB resources

Ebbe Sloth Andersen, Magnus Alm Rosenblad1,2, Niels Larsen3, Jesper Cairo Westergaard4, Jody Burks5, Iwona K. Wower5, Jacek Wower5, Jan Gorodkin6, Tore Samuelsson1 and Christian Zwieb7,*

Department of Molecular Biology, University of Aarhus C.F. Moellers Allé, Building 139, 8000 Aarhus, Denmark 1Department of Medical Biochemistry, Goteborg University Box 440, SE-405 30 Goteborg, Sweden 2SWEGENE Bioinformatics, Goteborg University Box 413, SE-405 30 Goteborg, Sweden 3Danish Genome Institute Gustav Wieds vej 10 C, DK-8000 Aarhus C, Denmark 4Department of Natural Sciences, The Royal Veterinary and Agricultural University Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark 5Department of Animal Sciences, Auburn University Auburn, AL 36849-5415, USA 6Center for Bioinformatics and Division of Genetics, IBHV, The Royal Veterinary and Agricultural University Groennegaardsvej 3, 1870 Frederiksberg C, Denmark 7Department of Molecular Biology, The University of Texas Health Science Center at Tyler 11937 US Highway 271, Tyler, TX 75708-3154, USA

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

Received September 15, 2005. Revised October 27, 2005. Accepted October 27, 2005.

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 Royal Veterinary and Agricultural University, Denmark (http://tmrdb.kvl.dk/). The signal recognition particle database (SRPDB) at http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html is mirrored at http://srpdb.kvl.dk/ and the University of Goteborg (http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html). The databases assist in investigations of the tmRNP (a ribonucleoprotein complex which liberates stalled bacterial ribosomes) and the SRP (a particle which recognizes signal sequences and directs secretory proteins to cell membranes). The curated tmRNA and SRP RNA alignments consider base pairs supported by comparative sequence analysis. Also shown are alignments of the tmRNA-associated proteins SmpB, ribosomal protein S1, alanyl-tRNA synthetase and Elongation Factor Tu, as well as the SRP proteins SRP9, SRP14, SRP19, SRP21, SRP54 (Ffh), SRP68, SRP72, cpSRP43, Flhf, SRP receptor (alpha) and SRP receptor (beta). All alignments can be easily examined using a new exploratory browser. The databases provide links to high-resolution structures and serve as depositories for structures obtained by molecular modeling.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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