Semi-automated update and cleanup of structural RNA alignment databases

We have developed a series of programs which assist in maintenance of struc tural 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, oth er programs can examine base pair consistency and phylogenetic support. The output can be applied iteratively to refine the structural alignment of th e RNA database. Using these tools, the number of potential misannotations p er sequence was reduced from 20 to 3 in the Signal Recognition Particle RNA database.