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

J. Gorodkin, C. Zwieb, B. Knudsen

Research output: Contribution to journal › Article › peer-review

14 Scopus citations

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.

Original language	English (US)
Pages (from-to)	642-645
Number of pages	4
Journal	Bioinformatics
Volume	17
Issue number	7
DOIs	https://doi.org/10.1093/bioinformatics/17.7.642
State	Published - 2001
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/17.7.642

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title = "Semi-automated update and cleanup of structural RNA alignment databases",

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.",

author = "J. Gorodkin and C. Zwieb and B. Knudsen",

note = "Funding Information: This work was supported by the Danish Technical Research Council (J.G.). J.G. thanks G. D. Stormo for support at Washington University Medical School in St Louis. We would like to thank E. Rivas and S. Eddy for the introduction to the qrna program, and anonymous reviewers for useful suggestions.",

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AU - Knudsen, B.

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Semi-automated update and cleanup of structural RNA alignment databases

Abstract

ASJC Scopus subject areas

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