Semi-automated update and cleanup of structural RNA alignment databases

J. Gorodkin, Christian W Zwieb, B. Knudsen

Research output: Contribution to journalArticle

14 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)642-645
Number of pages4
JournalBioinformatics
Volume17
Issue number7
StatePublished - 2001
Externally publishedYes

Fingerprint

Nucleic Acid Databases
RNA
Alignment
Update
Signal Recognition Particle
Phylogenetics
Base Pairing
Maintenance
Entire
Databases
Query
Series
Output
Range of data

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

Gorodkin, J., Zwieb, C. W., & Knudsen, B. (2001). Semi-automated update and cleanup of structural RNA alignment databases. Bioinformatics, 17(7), 642-645.

Semi-automated update and cleanup of structural RNA alignment databases. / Gorodkin, J.; Zwieb, Christian W; Knudsen, B.

In: Bioinformatics, Vol. 17, No. 7, 2001, p. 642-645.

Research output: Contribution to journalArticle

Gorodkin, J, Zwieb, CW & Knudsen, B 2001, 'Semi-automated update and cleanup of structural RNA alignment databases', Bioinformatics, vol. 17, no. 7, pp. 642-645.
Gorodkin, J. ; Zwieb, Christian W ; Knudsen, B. / Semi-automated update and cleanup of structural RNA alignment databases. In: Bioinformatics. 2001 ; Vol. 17, No. 7. pp. 642-645.
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