RATT: Rapid annotation transfer tool

Otto, T. D. , Dillon, G. P., Degrave, W. S. and Berriman, M. (2011) RATT: Rapid annotation transfer tool. Nucleic Acids Research, 39(9), -. e57. (doi: 10.1093/nar/gkq1268) (PMID:21306991) (PMCID:PMC3089447)

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Abstract

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.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Otto, Dr Thomas
Authors: Otto, T. D., Dillon, G. P., Degrave, W. S., and Berriman, M.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Nucleic Acids Research
Publisher:Oxford University Press
ISSN:0305-1048
ISSN (Online):1362-4962
Copyright Holders:Copyright ©2011 The Authors
First Published:First published in Nucleic Acids Research 39(9):e57
Publisher Policy:Reproduced under a Creative Commons License

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