TY - JOUR
T1 - The tmRDB and SRPDB resources
AU - Andersen, Ebbe Sloth
AU - Rosenblad, Magnus Alm
AU - Larsen, Niels
AU - Westergaard, Jesper Cairo
AU - Burks, Jody
AU - Wower, Iwona K.
AU - Wower, Jacek
AU - Gorodkin, Jan
AU - Samuelsson, Tore
AU - Zwieb, Christian
N1 - Funding Information:
We thank Jorgen Kjems for RNA expertise and support, Allan Lind-Thomsen for assistance with SARSE and Florian Müller for the ERNA-3D modeling program. E.S.A. is supported by the Interdisciplinary Nanoscience Center (iNANO) of the University of Aarhus. M.A.R. is supported by the SWEGENE consortium. J.G. is supported by the Danish Research Council for Technology and Production Sciences and the Danish Center for Scientific Computing. This work was also supported by NIH grants GM-58267 to J.W. and GM-49034 to C.Z. Funding to pay the Open Access publication charges for this article was provided by NIH grant GM-49034 to C.Z.
Publisher Copyright:
© The Author 2006. Published by Oxford University Press.
PY - 2006/1
Y1 - 2006/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=33644876507&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33644876507&partnerID=8YFLogxK
U2 - 10.1093/nar/gkj142
DO - 10.1093/nar/gkj142
M3 - Article
C2 - 16381838
AN - SCOPUS:33644876507
VL - 34
SP - D163-D168
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
ER -