TiCo is a tool for postprocessing predictions of prokaryotic genes with the objective to improve the accuracy of annotated Translation Initiation Sites (TIS).
Currently the tool can be used to analyze and reannotate predictions obtained by the program GLIMMER2.x (Delcher et al., 1999). The underlying algorithm of TiCo is based on a completely unsupervised method for scoring potential translation starts. The method works without specific assumptions about characteristic sequence features such as Shine-Dalgarno motifs or start codon usage. In addition, empirical thresholds have been avoided in order to prevent the algorithm from specialization with respect to particular test data. View a detailed description of the algorithm.
TiCo provides a GLIMMER-like output which contains the relocated gene starts together with some information for the evaluation of the quality of the corresponding TIS. The results are also available in GFF (general feature format). View a detailed description of the output with examples.
Online submission form to TiCo's web interface.
Download commandline version of TiCo (Linux/Windows).
View some results obtained by TiCo.
Visualization of the weights matrix calculated by TiCo. View an example .
Please cite one of these publications if you use TICO for your results.
- Maike Tech, Nico Pfeifer, Burkhard Morgenstern, Peter Meinicke (2005). TICO: a tool for improving predictions of prokaryotic translation initiation sites. Bioinformatics 21, 3568 - 3569.
- Maike Tech and Peter Meinicke (2006). An unsupervised classification scheme for improving predictions of prokaryotic TIS. BMC Bioinformatics, 7, 121.
- Maike Tech, Burkhard Morgenstern, Peter Meinicke (2006). TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites. Nucleic Acids Res.,Web Server issue, 34.
Please direct your questions and comments to firstname.lastname@example.org.