Semi-automated update and cleanup of structural RNA alignment databases

J. Gorodkin, C. Zwieb, B. Knudsen

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


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
Issue number7
StatePublished - 2001
Externally publishedYes

ASJC Scopus subject areas

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


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