An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance

Background: Motif finding algorithms have developed in their ability to use computationally efficient methods to detect patterns in biological sequences. However the posterior classification of the output still suffers from some limitations, which makes it difficult to assess the biological significance of the motifs found. Previous work has highlighted the existence of positional bias of motifs in the DNA sequences, which might indicate not only that the pattern is important, but also provide hints of the positions where these patterns occur preferentially. Results: We propose to integrate position uniformity tests and over-representation tests to improve the accuracy of the classification of motifs. Using artificial data, we have compared three different statistical tests (Chi-Square, Kolmogorov-Smirnov and a Chi-Square bootstrap) to assess whether a given motif occurs uniformly in the promoter region of a gene. Using the test that performed better in this dataset, we proceeded to s...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Ana C. Casimiro, Susana Vinga, Ana T. Freitas, Arlindo L. Oliveira
• Keywords: BMCBI 2008, Dna Sequences, Promoter Region, Sequences