Introduction

MOTIVATION: Promoter prediction is important for the analysis of gene regulations. Although a number of promoter prediction algorithms have been reported in literature, significant improvement in prediction accuracy remains a challenge. In this paper, an effective promoter identification algorithm, which is called PromoterExplorer, is proposed. In our approach, we analyze the different roles of various features, that is, local distribution of pentamers, positional CpG island features and digitized DNA sequence, and then combine them to build a high-dimensional input vector. A cascade AdaBoost-based learning procedure is adopted to select the most 'informative' or 'discriminating' features to build a sequence of weak classifiers, which are combined to form a strong classifier so as to achieve a better performance. The cascade structure used for identification can also reduce the false positive. RESULTS: PromoterExplorer is tested based on large-scale DNA sequences from different databases, including the EPD, DBTSS, GenBank and human chromosome 22. Experimental results show that consistent and promising performance can be achieved.

Publications

  1. PromoterExplorer: an effective promoter identification method based on the AdaBoost algorithm.
    Cite this
    Xie X, Wu S, Lam KM, Yan H, 2006-11-01 - Bioinformatics (Oxford, England)

Credits

  1. Xudong Xie
    Developer

  2. Shuanhu Wu
    Developer

  3. Kin-Man Lam
    Developer

  4. Hong Yan
    Investigator

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT000277
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByHong Yan