Semi-automated update and cleanup of structural RNA alignment databases

• Published in: Bioinformatics 2001-07, Vol.17 (7), p.642-645
• Main Authors: Gorodkin, J., Zwieb, C., Knudsen, B.
• Format: Article
• Language: English
• Subjects: Base Sequence; Biological and medical sciences; Computational Biology; Databases as Topic; Fundamental and applied biological sciences. Psychology; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Molecular Sequence Data; RNA - genetics; RNA, Messenger - genetics; Sequence Alignment - statistics & numerical data; Sequence Analysis, RNA - statistics & numerical data; Sequence Homology, Nucleic Acid; Software
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/17.7.642

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: [e-mail] * These authors contributed equally to this work. † To whom correspondence should be addressed.