Semi-automated update and cleanup of structural RNA alignment databases

Bioinformatics. 2001 Jul;17(7):642-5. 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

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Computational Biology
  • Databases as Topic*
  • Molecular Sequence Data
  • RNA / genetics*
  • RNA, Messenger / genetics
  • Sequence Alignment / statistics & numerical data*
  • Sequence Analysis, RNA / statistics & numerical data
  • Sequence Homology, Nucleic Acid
  • Software


  • RNA, Messenger
  • RNA