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Nucleic Acids Research Advance Access originally published online on October 16, 2007
Nucleic Acids Research 2008 36(Database issue):D114-D119; doi:10.1093/nar/gkm799
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Nucleic Acids Research, 2008, Vol. 36, Database issue D114-D119
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes

Gang-Qing Hu1,2, Xiaobin Zheng1,2, Yi-Fan Yang1,2, Philippe Ortet3, Zhen-Su She1,2,4 and Huaiqiu Zhu1,2,*

1State Key Lab for Turbulence and Complex System and Department of Biomedical Engineering, 2Center for Theoretical Biology and Department of Physics, Peking University, Beijing 100871, China, 3CEA, DSV, IBEB, LEMiRE, CNRS, Université Aix-Marseille II, CEA Cadarache, F-13108 Saint-Paul-lez-Durance, France and 4Department of Mathematics, UCLA, Los Angeles, CA 90095, USA

* To whom correspondence should be addressed. Tel: 8610 6276 7261; Fax: 8610 6276 7261; Email: hqzhu{at}pku.edu.cn hqzhu{at}ctb.pku.edu.cn

Received August 15, 2007. Revised September 16, 2007. Accepted September 17, 2007.

Correct annotation of translation initiation site (TIS) is essential for both experiments and bioinformatics studies of prokaryotic translation initiation mechanism as well as understanding of gene regulation and gene structure. Here we describe a comprehensive database ProTISA, which collects TIS confirmed through a variety of available evidences for prokaryotic genomes, including Swiss-Prot experiments record, literature, conserved domain hits and sequence alignment between orthologous genes. Moreover, by combining the predictions from our recently developed TIS post-processor, ProTISA provides a refined annotation for the public database RefSeq. Furthermore, the database annotates the potential regulatory signals associated with translation initiation at the TIS upstream region. As of July 2007, ProTISA includes 440 microbial genomes with more than 390 000 confirmed TISs. The database is available at http://mech.ctb.pku.edu.cn/protisa


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