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Bioinformatics Advance Access originally published online on April 23, 2009
Bioinformatics 2009 25(14):1843-1845; doi:10.1093/bioinformatics/btp272
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction

Gang-Qing Hu {dagger}, Jiang-Tao Guo {dagger}, Yong-Chu Liu {dagger} and Huaiqiu Zhu *

State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering and Center for Theoretical Biology, Peking University, Beijing 100871, China

* To whom correspondence should be addressed.


  Abstract

Summary: We proposed a tool named MetaTISA with an aim to improve TIS prediction of current gene-finders for metagenomes. The method employs a two-step strategy to predict translation initiation sites (TISs) by first clustering metagenomic fragments into phylogenetic groups and then predicting TISs independently for each group in an unsupervised manner. As evaluated on experimentally verified TISs, MetaTISA greatly improves the accuracies of TIS prediction of current gene-finders.

Availability: The C++ source code is freely available under the GNU GPL license via http://mech.ctb.pku.edu.cn/MetaTISA/.

Contact: hqzhu{at}pku.edu.cn

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger} The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors.

Associate Editor: Limsoon Wong

Received on February 12, 2009; revised on April 17, 2009; accepted on April 17, 2009

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