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Nucleic Acids Research 2006 34(Web Server issue):W345-W349; doi:10.1093/nar/gkl283
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB

Chisato Yamasaki1,2, Hiroaki Kawashima1,3, Fusano Todokoro3, Yasuhiro Imamizu3, Makoto Ogawa3, Motohiko Tanino1,2, Takeshi Itoh2,4, Takashi Gojobori2,5,6 and Tadashi Imanishi2,*

1 Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics Consortium AIST Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan 2 Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology AIST Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan 3 DYNACOM Co., Ltd 643 Mobara, Mobara-shi, Chiba 297-0026, Japan 4 Genome Research Department, National Institute of Agrobiological Sciences 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan 5 Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics 1111 Yata, Mishima, Shizuoka 411-8540, Japan 6 Department of Genetics, The Graduate University for Advanced Studies 1111 Yata, Mishima Shizuoka 411-8540, Japan

*To whom correspondence should be addressed. Tel: +81 3 3599 8800; Fax: +81 3 3599 8801; Email: imanishi{at}jbirc.aist.go.jp

Received February 14, 2006. Revised February 25, 2006. Accepted April 5, 2006.

Transcriptome Auto-annotation Conducting Tool (TACT) is a newly developed web-based automated tool for conducting functional annotation of transcripts by the integration of sequence similarity searches and functional motif predictions. We developed the TACT system by integrating two kinds of similarity searches, FASTY and BLASTX, against protein sequence databases, UniProtKB (Swiss-Prot/TrEMBL) and RefSeq, and a unified motif prediction program, InterProScan, into the ORF-prediction pipeline originally designed for the ‘H-Invitational’ human transcriptome annotation project. This system successively applies these constituent programs to an mRNA sequence in order to predict the most plausible ORF and the function of the protein encoded. In this study, we applied the TACT system to 19 574 non-redundant human transcripts registered in H-InvDB and evaluated its predictive power by the degree of agreement with human-curated functional annotation in H-InvDB. As a result, the TACT system could assign functional description to 12 559 transcripts (64.2%), the remainder being hypothetical proteins. Furthermore, the overall agreement of functional annotation with H-InvDB, including those transcripts annotated as hypothetical proteins, was 83.9% (16 432/19 574). These results show that the TACT system is useful for functional annotation and that the prediction of ORFs and protein functions is highly accurate and close to the results of human curation. TACT is freely available at http://www.jbirc.aist.go.jp/tact/.


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