D694 Nucleic Acids Research, 2006, Vol. 34, Database issue Figure 1. ChloroplastDB overview. (A) Database structure and relationship of data tables. PK: primary key. FK: foreign key. (B) Data flow and filtering steps to ensure the high quality of data stored in the database. in other plants including tobacco, maize and Adiantum chloro- plast DNA. Because the GenBank record does not contain a standard feature to store the RNA editing information, some edited sites were not reported while others were reported as exceptions since the protein sequence did not match concep- tual translation of the protein coding gene. To maintain quality and consistency of the data, we report annotated locations and the edited mRNA sequence. THE CHLOROPLAST GENOME DATABASE INTERFACE Web user interfaces, developed using Perl CGI scripts, interact with the above mentioned data repository and provide users with basic sequence analysis tools (Figure 2). ChloroplastDB can be queried by gene name, and query results are returned in a table with links to individual genes. The BLAST similarity search was implemented for search against whole genome, extracted proteins or extracted CDS. Sequences returned in BLAST searches can be exported to a fasta ﬁle. A user can also browse the list of organisms and all genes by speciﬁed sub- types (tRNA, rRNA and protein-coding) from each organism. The set of extracted genes vary from 56 in a non- photosynthetic parasitic plant, Epifagus virginiana, to 254 in the red alga Porphyra purpurea, including duplicate genes that are present in the genome. Tribes represent putat- ively orthologous genes across organisms, which can be down- loaded to construct multiple sequence alignments. Together,