Finding Transcription Factor Binding Sites with Indels

Finding transcription factor binding sites is of great importance for biologists to understand gene expression regulatory mechanisms. Usually, researchers design algorithms to detect transcription factor biding sites with substitution mutations only, based on the conserved property of biological functional sequences. In this paper, we propose a randomized algorithm to find biding sites with indels. A tool is also developed to evaluate the performance of the algorithm based on simulated datasets.