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

Tcherepanov, Vasily; Ehlers, Angelika; Upton, Chris

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 size from 134 -360 kb; 3) more than 125 SARS genomes submitted since the first two SARS coronavirus genomes were published in May, 2003. The fact that the value of genomic data extends far beyond its use in an original publication is the foundation of data mining experiments. Unfortunately, however, a large number of the complete virus genomes submitted to Gen-Bank lack annotations, severely limiting the usefulness of the data. The subsequent annotation of these genomes by multiple researchers, who may lack bioinformatics experience, is a tedious and time-consuming process. In order to facilitate the process of annotation, we have developed a tool, Genome Annotation Transfer Utility (GATU), which makes use of the fact that most unannotated genomes are closely related to previously annotated genomes. The application can be run on most major operating systems including Mac OS X, Windows and Linux.