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Bioinformatics Vol. 17 no. 7 2001
Pages 642-645
© 2001 Oxford University Press

Semi-automated update and cleanup of structural RNA alignment databases

J. Gorodkin 1,*,{dagger}, C. Zwieb 2 and B. Knudsen 1,*

1 Department of Ecology and Genetics, The Institute of Biological Sciences, University of Aarhus, Building 540, Ny Munkegade, DK-8000 Aarhus C, Denmark
2 The University of Texas Health Science Center, 11937 US Highway 271, PO Box 2003, Tyler, TX 75708, USA

Received on November 10, 2000 ; revised on February 6, 2001 ; accepted on March 6, 2001

Summary: We have developed a series of programs which assist in maintenance of structural RNA databases. A main program BLASTs the RNA database against GenBank and automatically extends and realigns the sequences to include the entire range of the RNA query sequences. After manual update of the database, other programs can examine base pair consistency and phylogenetic support. The output can be applied iteratively to refine the structural alignment of the RNA database. Using these tools, the number of potential misannotations per sequence was reduced from 20 to 3 in the Signal Recognition Particle RNA database.

Availability: A quick-server and programs are available at http://www.bioinf.au.dk/rnadbtool/

Contact: gorodkin{at}bioinf.au.dk

* These authors contributed equally to this work.

{dagger} To whom correspondence should be addressed.


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