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

Resultado de la investigación: Article › revisión exhaustiva

14 Citas (Scopus)

Resumen

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.

Idioma original	English (US)
Páginas (desde-hasta)	642-645
Número de páginas	4
Publicación	Bioinformatics
Volumen	17
N.º	7
DOI	https://doi.org/10.1093/bioinformatics/17.7.642
Estado	Published - 2001
Publicado de forma externa	Sí

ASJC Scopus subject areas

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

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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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Semi-automated update and cleanup of structural RNA alignment databases

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ASJC Scopus subject areas

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