PROPER Reference

Contents

Introduction

Operation

Note

Reference

1. Introduction: What is PROPER

PROPER provides a graphic user interface (GUI) for operon prediction with the self-study algorithm. It has the following features:

n Operon Prediction: Based on the self-study algorithm[1], PROPER can predict operons among the sequenced bacterium with high sensitivity and specificity. Besides, with algorithms on promoter and terminator prediction, PROPER can also estimate the alternative operons or transcript units.

n Graphic User Interface: PROPER is built on Qt Creator, a cross-platform, complete integrated development environment (IDE). With Qt's advantages, PROPER provides a convenient user interface, especially for the genome/operon/tanscript unit's visualization.

2. Operation: How to use PROPER

2.1 PROPER can predict OPERON with the following operations:

n Load fna/ptt/rnt file of the same organism;

n Click the "Run" icon to begin prediction;

The progress bar shows the prediction degree. Once the prediction finished, PROPER shows the graphic results (Figure 1).

Figure 1 Graphic Results of Prediction

Double click the tree widget item in "Operon Information" field, the corresponding operon structure information would be show in the "Gene Information" field, including gene and sequence information (Figure 2, 3).

Figure 2 Visualization of the gene and operon

Figure 3 Gene information corresponding to the item

2.2 PROPER can view the predicted organism at any time.

n Make sure the all the relating files ( including ptt/rnt/fna, prediction result files ) are in the same directory. Use "Change Directory" can choose the working directory.

n Make sure loading fna/ptt/rnt file of the same organism ( here we take B. sub, NC_000964 as example);

n Click the "(Prediction Result)" icon to view prediction result;

3. Note: Understand PROPER

nPROPER consists of two major areas, including "Operon Information" and "Gene Information". It has the following features:

Figure 4 PROPER Structure

Figure 5 Notes for Prediction Results

n If you want to know more detail about the transcription unit, such as the terminator prediction result, promoter prediction result, and operon prediction result, you can locate the corresponding files in the ./result directory.

n Please feel free to direct your questions and suggestions to yce@pku.edu.cn.

4. Reference

[1] WU Wen-Qi, ZHENG Xiao-Bin, LIU Yong-Chu, TANG Kai, ZHU Huai-Qiu*. Operon prediction based on an iterative self-learning algorithm. Prog. Biochem. Biophys., 2011, 38(7): 642-651.