D696 Nucleic Acids Research, 2006, Vol. 34, Database issue also become a discovery tool for unannotated proteins. For example, ORF288 in hornwort, A.formosae, was sorted to the cysT tribe, together with an unannotated orthologous sequence from liverwort, Marchantia polymorpha. We also provide pre- computed protein and DNA alignments for each tribe. Whole genome comparison and batch sequence retrieval The plastid genomes from land plants, green algae, red algae and Apicomplexian represents a great range of diversity of the organelle genomes. The organism page presents direct link to the GenBank genome sequences, and ability to download gen- ome sequences and genes by organisms. The user can use the downloaded sequence for organism speciﬁc analysis, or com- parison for a speciﬁc type of sequences across organisms. FUTURE PROSPECTS Over the next few years, the growth of full organelle genome sequences will provide new opportunities for whole-genome comparative analyses. Cross-species investigations of genome-wide structural evolution, context-speciﬁc substitu- tion processes (33), RNA editing, gene regulation and gene function will be more tractable for organelle genomes than much larger and more complex nuclear genomes. Organelle genomes may be an ideal proving ground for methods of analysis being developed to understand genome and gene order evolution. The mission of ChloroplastDB is to pro- mote comparative analyses of plastid genomes by addressing the community need for better, uniform annotation, quick sequence retrieval and homology search tools. The function- ality of ChloroplastDB will grow as new genomes, alignments and other analyses are added, gene clustering techniques are improved, and visualization tools with gene order browsers are developed. ACKNOWLEDGEMENTS The authors thank Kevin Beckmann and Stacia Wyman for programming support, and Paul Wolf for providing RNA edit- ing information. 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