Semi-automated update and cleanup of structural RNA alignment databases

J Gorodkin; C Zwieb; B Knudsen

doi:10.1093/bioinformatics/17.7.642

Semi-automated update and cleanup of structural RNA alignment databases

Bioinformatics. 2001 Jul;17(7):642-5. doi: 10.1093/bioinformatics/17.7.642.

Authors

J Gorodkin¹, C Zwieb, B Knudsen

Affiliation

¹ Department of Ecology and Genetics, The Institute of Biological Sciences, University of Aarhus, Building 540, Ny Munkegade, DK-8000 Aarhus C, Denmark.

PMID: 11448882
DOI: 10.1093/bioinformatics/17.7.642

Abstract

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/

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Computational Biology
Databases as Topic*
Molecular Sequence Data
RNA / genetics*
RNA, Messenger / genetics
Sequence Alignment / statistics & numerical data*
Sequence Analysis, RNA / statistics & numerical data
Sequence Homology, Nucleic Acid
Software

Substances

RNA, Messenger
RNA