RATT: Rapid Annotation Transfer Tool

By Thomas D. Otto, Gary P. Dillon, W. Degrave, Matthew Berriman. Nucleic Acids Research, 2011

320 citations recorded by the source corpus.

Second-generation sequencing technologies have made large-scale sequencing projects commonplace. However, making use of these datasets often requires gene function to be ascribed genome wide. Although tool development has kept pace with the changes in sequence production, for tasks such as mapping, de novo assembly or visualization, genome annotation remains a challenge. We have developed a method to rapidly provide accurate annotation for new genomes using previously annotated genomes as a reference. The method, implemented in a tool called RATT (Rapid Annotation Transfer Tool), transfers annotations from a high-quality reference to a new genome on the basis of conserved synteny. We demonstrate that a Mycobacterium tuberculosis genome or a single 2.5 Mb chromosome from a malaria parasite can be annotated in less than five minutes with only modest computational resources. RATT is available at http://ratt.sourceforge.net.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/d9c18c109c465b40027be977738ba2d7797accb7

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In Molecular Biology

Citations in the corpus

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. (2012, background): “org/ RATT [41] VMGAP [31] CAMERA [42] METAREP [43]”
WormBase 2016: expanding to enable helminth genomic research (2015, unknown): “For the remaining genomes, we used MAKER2 (11) to generate high-quality annotations by integrating evidence from multiple sources: ab initio gene predictions from AUGUSTUS (12), GeneMarkES (13) and SNAP (14); projected annotations from C. elegans and the taxonomically nearest previously-annotated he”