In the case of the first type of input (FASTA file), the RAST Server will perform de novo annotation, i.e., will start by calling RNA-and protein-coding genes, and then will proceed to functional annotation, subsystems assignment, and subsequent metabolic reconstruction. In the second case (GenBank-formatted files), gene calling is optional, since GenBank-formatted files already include the coordinates for open-reading frames and RNA genes. In the last case (Entrez ID or Genome Project ID), the tools provided within the RAST Submission/Retrieval Server will query NCBI using the query ID(s) and will retrieve the sequence (whether that sequence consists of one or a set of contigs that make up the genome project); that sequence then becomes the input to the RAST Server.