Using Atlas in genome annotation. Atlas facilitates genome annotation at multiple levels: creation of data reagents, storage of annotations, and data transformation for submission. Here we show a schema of our genome annotation process that integrates Pegasys, Apollo, NCBI tools and Atlas into a comprehensive platform. Data reagents for sequence alignment are compiled using the Atlas toolbox applications. Computational analyses are run through the Pegasys system which outputs GAME XML for import into Apollo. Annotations are saved in a GAME XML which are then imported into Atlas using the GameLoader. At this step, the biological features created in the annotation process are stored in the Atlas Feature tables, exactly the same way a GenBank sequence record containing annotations are stored. These annotations can then be retrieved using the Atlas toolbox application ac2feat and exported in GFF2 or Sequin Feature Table Format for import into the NCBI submission tools for validation, and submission to GenBank.