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. 2006 Jul 1;34(Web Server issue):W588-90.
doi: 10.1093/nar/gkl313.

TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites

M Tech  1 , B Morgenstern, P Meinicke
Affiliations

TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites

M Tech et al. Nucleic Acids Res. .

Abstract

Exact localization of the translation initiation sites (TIS) in prokaryotic genomes is difficult to achieve using conventional gene finders. We recently introduced the program TICO for postprocessing TIS predictions based on a completely unsupervised learning algorithm. The program can be utilized through our web interface at http://tico.gobics.de/ and it is also freely available as a commandline version for Linux and Windows. The latest version of our program provides a tool for visualization of the resulting TIS model. Although the underlying method is not based on any specific assumptions about characteristic sequence features of prokaryotic TIS the prediction rates of our tool are competitive on experimentally verified test data.

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Figures

Figure 1
Figure 1
The submission page of the TICO web interface. The sequence and an annotation have to be uploaded. The user may choose one or more output formats and should give an email address to receive the results. In addition, some optional parameters can be adjusted, including the range of extracted sequences around the start candidates.
Figure 2
Figure 2
Visualization of the PWM calculated for E.coli using the default settings. On the horizontal axis the position within the sequence window is denoted; on the vertical axis trinucleotides are denoted in alphabetical order. The potential start codon is located at position 0. The upstream and downstream regions are represented by negative and positive position indices, respectively. A colour scale indicates the numerical values of the weights.
See this image and copyright information in PMC

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