tailieunhanh - Báo cáo sinh học: "Periodic pattern detection in sparse boolean sequences"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: Periodic pattern detection in sparse boolean sequences. | Junier et al. Algorithms for Molecular Biology 2010 5 31 http content 5 1 31 AMR ALGORITHMS FOR MOLECULAR BIOLOGY SOFTWARE ARTICLE Open Access Periodic pattern detection in sparse boolean sequences Ivan Junier1 2 Joan Hérisson 2 Frangois Képès2 Abstract Background The specific position of functionally related genes along the DNA has been shown to reflect the interplay between chromosome structure and genetic regulation. By investigating the statistical properties of the distances separating such genes several studies have highlighted various periodic trends. In many cases however groups built up from co-functional or co-regulated genes are small and contain wrong information data contamination so that the statistics is poorly exploitable. In addition gene positions are not expected to satisfy a perfectly ordered pattern along the DNA. Within this scope we present an algorithm that aims to highlight periodic patterns in sparse boolean sequences . sequences of the type 010011011010. where the ratio of the number of 1 s denoting here the transcription start of a gene to 0 s is small. Results The algorithm is particularly robust with respect to strong signal distortions such as the addition of 1 s at arbitrary positions contaminated data the deletion of existing 1 s in the sequence missing data and the presence of disorder in the position of the 1 s noise . This robustness property stems from an appropriate exploitation of the remarkable alignment properties of periodic points in solenoidal coordinates. Conclusions The efficiency of the algorithm is demonstrated in situations where standard Fourier-based spectral methods are poorly adapted. We also show how the proposed framework allows to identify the 1 s that participate in the periodic trends . how the framework allows to allocate a positional score to genes in the same spirit of the sequence score. The software is available for public use at http MEGA Softwares .