Nucleic Acids Research, 2006, Vol. 34, Database issue D695 Figure 2. Examples of analysis using the ChloroplastDB web interface. (A) Homepage of the database. (B) Search results for the gene ‘rbcL’. (C) The gene view page linked to search result for each gene, including mRNA editing information. (D) BLAST results, with options to download sequences from the BLAST search. (E) Putative orthologous gene set listed as ‘Tribes’. (F) The organism page presents a summary of genomes and extracted features in the database for batch download. these web interfaces provides a workbench for query, search, and sequence compilation and analysis. The various functions are seamlessly linked for a smooth user experience. HOW TO USE THE CHLOROPLAST DATABASE Gene search The basic query page allows a user to search for individual gene of interest. For example, search of ‘rbcL’ returns all rbcL gene entries, in which two copies are from Nephroselmis olivacea since they are duplicated and located in the inverted repeats. Each gene is then linked to a gene view page. The gene view displays the gene name, organism, coordinates on the genome, exon boundaries, and DNA or protein sequences. Annotated RNA edits are highlighted with colours for easy identiﬁcation. BLAST Customized BLAST searches against nucleotide CDS, pro- teins or genomic sequences allows a researcher to quickly identify novel sequences, to construct alignments and to annot- ate chloroplast genes. The returned entries are linked to respective gene view page or the whole genome record in NCBI. Selected list of entries can be exported as fasta sequences. A user can also run BLAST against the Arabidopsis or rice proteome to identify nuclear encoded homologs of chloroplast genes. Tribes An important feature of this database is pre-computed ortho- logous protein sets, which could be used for phylogenetic analysis. The tribes present a uniform, automatic classiﬁcation of chloroplast proteins using MCL clustering on all-by-all BLAST search results. With few exceptions, all other tribes represent orthologous gene sets, and a standard name is dis- played for each tribe according to the UniProt list of plastid and cyanelle genes. The paralogous psaA and psaB are highly similar duplicate genes (BLAST E-value < 1.0E 150) which are grouped together in a single tribe. In contrast, rapidly evolving ycf1 genes are split into three tribes including seed plant, ferns plus bryophytes and algal orthologues. Tribes