ProTISA is intended to collect confirmed translation initiation sites (TISs) for prokaryotic genomes. As of Oct 2008, it includes data for 728 genomes (676 Bacteria and 52 Archaea) with more than 700, 000 confirmed TISs.

   The confirmed data  has supporting evidence from different sources, including experiments records in the public protein database Swiss-Prot, literature, conserved domain search and sequence alignment among orthologous genes. Combing with predictions from the-state-of-the-art TIS predictor MED-Start/MED-StartPlus (in release 1.0 & 1.2) and TriTISA (since release 1.4) and annotations on potential regulatory signals, the database can serve as a refined annotation resource for the public database RefSeq.

Access

The database can be retrieved via

　

  • Search search by region in the genome sequence, gene name and PID

  • Browse  refined TIS annotation for the whole genome

  • Download download annotations in Flat Files (prepared for SQL) as well as source code

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    Related databases

    Alternative Translational Initiation Database http://bioinfo.au.tsinghua.edu.cn/atie/

    Database of mRNA sequence with non-AUG start codon http://bioinfo.iitk.ac.in/bioinfo/

    Translation Initiation Sites and Secretory Targets http://ipe.cbmeg.unicamp.br/pub/TISs-ST/

    Citation

    Hu, G.-Q., Zheng, X., Yang, Y.-F., Ortet, P., She, Z.-S. and Zhu, H. (2008) ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes. Nucleic Acids Research, 36:D114-D119
    References

    1. Bailey, T.L. and Elkan, C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers, Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB, 2, 28-36.

    2. Frishman, D., Mironov, A., Mewes, H.W., and Gelfand, M. (1998) Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. Nucleic Acids Research 26:2941-2947.

    3. Makita, Y. De Hoon MJL and Danchin, A. (2007) Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes. MBC Bioinformatics 8:47.

    4. Torarinsson, E., Klenk, H.P., Garrett, R.A. (2005) Divergent transcriptional and translational signals in Archaea. Environmental microbiology 2005, 7:47-54.

    MED gene prediction series

    1. Ouyang, Z.,  Zhu, H.Q., Wang, J. and She, Z.-S. (2004) Multivariate entropy distance method for prokaryotic gene identification. Journal of Bioinformatics and Computational Biology, 2: 353-373. (MED 1.0)

    2. Zhu, H.Q., Hu, G.-Q., Ouyang, Z., Wang, J. and She, Z.-S. (2004) Accuracy improvement for identifying translation initiation sites in microbial genomes. Bioinformatics 20:3308-3317. (MED-Start)

    3. Zhu, H.Q., Hu, G.-Q., Yang, Y.-F., Wang, J. and She, Z.-S. (2007) MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes. BMC Bioinformatics, 8:97. (MED 2.0)

    4. Hu, G.Q., Liu, Y.C., Zheng, X.B., Yang, Y.F., She, Z.S., and Zhu, H.Q. (2008) New solutions of translation initiation site prediction for prokaryotic genomes. Progress in Biochemistry and Biophysics, 35(11): 1254-1262. (MED-StartPlus)

    TISA series on start finding for bacterial genomes

    1. Hu, G.Q., Zheng, X.B., Yang, Y.F., Ortet, P., She, Z.S., and Zhu, H.Q. (2008) ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes. Nucleic Acids Research, 36:D114-D119. (ProTISA)

    2. Hu, G.Q., Zheng, X.B., Ju, L.N., Zhu, H.Q., and She, Z.S. (2008) Computational evaluation of TIS annotation for prokaryotic genomes. BMC Bioinformatics, 9:160. (SupTISA)

    3. Hu, G.Q., Zheng, X.B., Zhu, H.Q., and She, Z.S. (2009) Prediction of translation initiation site for microbial genomes with TriTISA. Bioinformatics, 25(1): 123-125. (TriTISA)

    4. Hu, G.Q., Guo, J.T., Liu, Y.C., and Zhu, H.Q. (2009) MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction. Bioinformatics (in press). (MetaTISA)
    Last update on Dec. 2008, Copyright(C)2007, All Rights Reserved