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: WordCluster: detecting clusters of DNA words and genomic elements. | Hackenberg et al. Algorithms for Molecular Biology 2011 6 2 http content 6 1 2 AMR ALGORITHMS FOR MOLECULAR BIOLOGY SOFTWARE ARTICLE Open Access WordCluster detecting clusters of DNA words and genomic elements 1 23 2 1 1 Michael Hackenberg Pedro Carpena Pedro Bernaola-Galván Guillermo Barturen Ángel M Alganza José L Oliver 1 Abstract Background Many k-mers or DNA words and genomic elements are known to be spatially clustered in the genome. Well established examples are the genes TFBSs CpG dinucleotides microRNA genes and ultra-conserved non-coding regions. Currently no algorithm exists to find these clusters in a statistically comprehensible way. The detection ofclustering often relies on densities and sliding-window approaches or arbitrarily chosen distance thresholds. Results We introduce here an algorithm to detect clusters of DNA words k-mers or any other genomic element based on the distance between consecutive copies and an assigned statistical significance. We implemented the method into a web server connected to a MySQL backend which also determines the co-localization with gene annotations. We demonstrate the usefulness of this approach by detecting the clusters of CAG CTG cytosine contexts that can be methylated in undifferentiated cells showing that the degree of methylation vary drastically between inside and outside of the clusters. As another example we used Wordcluster to search for statistically significant clusters of olfactory receptor OR genes in the human genome. Conclusions Wordcluster seems to predict biological meaningful clusters of DNA words k-mers and genomic entities. The implementation of the method into a web server is available at http wordCluster including additional features like the detection of co-localization with gene regions or the annotation enrichment tool for functional analysis of overlapped genes. Background Genome entities as diverse as genes 1 CpG dinucleotides 2 transcription
