RATT: Rapid Annotation Transfer Tool

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,...

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Bibliographic Details
Published inNucleic acids research Vol. 39; no. 9; p. e57
Main Authors Otto, Thomas D, Dillon, Gary P, Degrave, Wim S, Berriman, Matthew
Format Journal Article
LanguageEnglish
Published England Oxford University Press 01.05.2011
Subjects
Algorithms
Genome, Bacterial
Genome, Protozoan
Genomics - methods
Methods Online
Molecular Sequence Annotation - methods
Mycobacterium tuberculosis
Mycobacterium tuberculosis - genetics
Plasmodium berghei - genetics
Plasmodium chabaudi - genetics
Software
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Summary: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.
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ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkq1268