Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome

GATU transfers annotations from a reference genome to a closely related target genome, while still giving the user final control over which annotations should be included. GATU also detects open reading frames present in the target but not the reference genome and provides the user with a variety of bioinformatics tools to quickly determine if these ORFs should also be included in the annotation. After this process is complete, GATU saves the newly annotated genome as a GenBank, EMBL or XML-format file. The software is coded in Java and runs on a variety of computer platforms. Its user-friendly Graphical User Interface is specifically designed for users trained in the biological sciences.GATU greatly simplifies the initial stages of genome annotation by using a closely related genome as a reference. It is not intended to be a gene prediction tool or a "complete" annotation system, but we have found that it significantly reduces the time required for annotation of genes and mature peptides as well as helping to standardize gene names between related organisms by transferring reference genome annotations to the target genome.The program is freely available under the General Public License and can be accessed along with documentation and tutorial from http://www.virology.ca/gatu webcite.With recent advances in DNA sequencing technology and reductions in sequencing costs, it has become relatively easy to sequence the complete genomes of many viruses and it is not uncommon for researchers to determine the sequence of multiple virus isolates as part of a single experiment. Although this ability to gather larger collections of genome sequences has opened up new avenues of research, it has also led to significant problems related to data management and sequence annotation. Examples of this data explosion include the following, all found in GenBank: 1) 1201 nearly complete genomes of human immunodeficiency virus (HIV); 2) 53 complete poxvirus genomes, with genomes ranging in