A gene order database of plastid genomes

Abstract

A gene order database of 32 completely sequenced plastid genomes was developed. The data structure is formally identical to that of the feature tables in the major GenBank/EMBL/DDBJ databases. The quality of annotations was largely improved. A normalizing gene-labeling system across the complete plastid genomes was developed so that comparative studies are made available without having to go back to sequence analysis. Many incorrect coordinates of tRNA-encoding regions found in the major databases were corrected. We attempted to distinctively label tRNA genes with the anticodon sequence CAT, which encodes either the initiator tRNA, elongator tRNA, or Ile-tRNA. The database is available at http://www.rs.noda.tus.ac.jp/~kunisawa.