DOGMA is a web-based tool for automatically annotating organellar genomes, specifically plant chloroplast and animal mitochondrial genomes. It uses BLAST searches against custom databases and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes. DOGMA provides a graphical user interface for viewing and editing annotations, which are stored on a password-protected server for repeated sessions. Completed annotations can be exported for submission to GenBank. DOGMA uses BLAST searches to identify protein-coding genes by comparing sequence similarity to genes in other genomes. For ribosomal RNA (rRNA) and transfer RNA (tRNA), it uses nucleotide sequence databases. The tool identifies tRNA anticodons based on database entries. For animal mitochondrial tRNAs, which diverge rapidly, DOGMA uses hidden Markov models and the COVE program to infer secondary structure. It also identifies rRNAs through BLAST searches, with optimized parameters for mitochondrial genomes. DOGMA is a web-based display and editing tool that allows users to create user IDs and passwords to keep their data private. It displays putative genes in a three-panel interface, with details for annotation in the top panel and a new window for input to Sequin. Users can select start and stop codons for genes, and annotate rRNAs and chloroplast tRNAs by choosing start and end positions. DOGMA also displays the putative secondary structure of tRNAs. Future work includes expanding the chloroplast database to include more taxa and adding mitochondrial genomes of plants, fungi, and protists to DOGMA. It also plans to include private custom databases and a searchable database of folded tRNA structures. DOGMA will also address RNA editing of start and stop codons and include an ORF finder for identifying new genes.DOGMA is a web-based tool for automatically annotating organellar genomes, specifically plant chloroplast and animal mitochondrial genomes. It uses BLAST searches against custom databases and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes. DOGMA provides a graphical user interface for viewing and editing annotations, which are stored on a password-protected server for repeated sessions. Completed annotations can be exported for submission to GenBank. DOGMA uses BLAST searches to identify protein-coding genes by comparing sequence similarity to genes in other genomes. For ribosomal RNA (rRNA) and transfer RNA (tRNA), it uses nucleotide sequence databases. The tool identifies tRNA anticodons based on database entries. For animal mitochondrial tRNAs, which diverge rapidly, DOGMA uses hidden Markov models and the COVE program to infer secondary structure. It also identifies rRNAs through BLAST searches, with optimized parameters for mitochondrial genomes. DOGMA is a web-based display and editing tool that allows users to create user IDs and passwords to keep their data private. It displays putative genes in a three-panel interface, with details for annotation in the top panel and a new window for input to Sequin. Users can select start and stop codons for genes, and annotate rRNAs and chloroplast tRNAs by choosing start and end positions. DOGMA also displays the putative secondary structure of tRNAs. Future work includes expanding the chloroplast database to include more taxa and adding mitochondrial genomes of plants, fungi, and protists to DOGMA. It also plans to include private custom databases and a searchable database of folded tRNA structures. DOGMA will also address RNA editing of start and stop codons and include an ORF finder for identifying new genes.