EcologicalGenomics.ppt

生物信息学中的几个计算问题简介 林魁 Laboratory of Computational Molecular Biology [] College of Life Sciences Beijing Normal University Some models Dynamic programming Hidden Markov Models (HMMs) Conditional random field (CRF) Support vector machines (SVMs) gbrowser Phylogenetics Evolutionary theory states that groups of similar organisms are descended from a common ancestor. Phylogenetic systematics (cladistics) is a method of taxonomic classification based on their evolutionary history. It was developed by Willi Hennig, a German entomologist, in 1950. Major reasons to use phylogenetics Understand the lineage of different species Organizing principle to sort species into a taxonomy Understand how various functions evolved Understand forces and constraints on evolution Perform multiple sequence alignment Predict gene function (phylogenetic footprint) Species/Gene Trees Species tree (how are my species related?) contains only one representative from each species when did speciation take place? all nodes indicate speciation events Gene tree (how are my genes related?) often contains a number of genes from a single species. nodes relate either to speciation or gene duplication events. Species tree Phylogenomics: Genome trees Explore genome evolution based on large data sets of DNA or protein sequences. Using entire genomes to infer a species tree (Eisen and Fraser 2003). Based on maximum genetic information and average out the anomalies. Has become the standard for reconstructing reliable phylogenies (Ciccarelli et al, 2006; Daubin et al. 2002). Taxonomic resolution of some of the novel approaches Creating ever-more robust phylogenies on the basis of diverse data sets. Evolutionary theory is evolving Metagenomics offers a way forward Who is out there? What are they doing? ? What is being done by the community? Broad-range PCR amplification and sequencing of microbial 16S rRNA genes Microbial diversity in environmental samples 拟展开的工作 不同生境（或样本）的群落基因组间比较分析，具体阐明关键环境因子的改变如何导