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 |
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Status: | Published |
Refereed: | Yes |
Glasgow Author(s) Enlighten ID: | Otto, Professor Thomas |
Authors: | Otto, T. D., Dillon, G. P., Degrave, W. S., and Berriman, M. |
College/School: | College of Medical Veterinary and Life Sciences > School of Infection & Immunity |
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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