转录与重建.ppt

转录分析与重建 捕获表达的转录本 数据库 –序列 dbEST Several collapsed datasets TIGR-THC Allgenes Unigene BodyMap STACK Several more specialized Genome sequence as it appears: 表达捕获 基因表达连续分析 DNA片段作为基因表达的特异标记。 检验一组序列中每种标记的数量可以度量基因表达。 列阵 Laydown of sequence clones to provide an organized series for hybridization ESTs有什么潜在作用? 表达计算 Consensus sequences 选择性表达特征 Identification of genes expressed in a pilot gene discovery project 在给定的基因文库或组织中识别出特异表达基因。 全基因组中使用转录本 基因辨识 外显子边界 选择性剪辑 基因组注释 编码基因表达位点 比较基因组学 EST数据的质量 Overview of clustering and consensus generation 什么是EST簇? “A cluster is fragmented, EST data and (if known) composite exon transcript sequence data, consolidated, placed in correct context and indexed by gene such that all expressed data concerning a single gene is in a single index class, and each index class contains the information for only one gene.” 宽松和严格聚类 严格聚类 – 高精确度、低覆盖度 One pass Shorter consensi Lower inclusion rate of expression-forms 宽松聚类 – 低精确度、高覆盖度 Multi-pass Longer consensus sequences but paralogs need attention Comprehensive inclusion of expression-forms 监督聚类（Supervised clustering） 作为“杂交模版（template for hybridization） ” 的转录本来源如下： 捕获的“全长” mRNA 由基因组序列而来的合成外显子 An assembled EST cluster consensus Clean short and tight 数据理解及输入格式 来源：内部、公共、私人的 ‘Accession’ / Sequence-run ID Location/orientation Source clone Source library and conditions 预处理 最小化信息长度 低复杂性区域 去除共有污染 Vector, repeats, mitochondrial, xenocontaminants XBLAST, Repeatmasker, VecBase and others BLIND masking Pre-clustering vs. known transcripts 最初聚类 Stepwise clustering ‘Multistate’ Sequence identity Annotation verification 装配 包括层析图 – SNPs and paralogs PHRAP and CAP series Multiple assemblies can fragment from one input cluster Fidelity Alt. forms error 比对过程 Consensus generation Alternate forms Errors Choosing the ‘correct consensus’ Cluster joining Clone joining Choosing to accept a clone annotation 1 Clone ID 2 Clone ID’s Available parents mRNA (incomplete/alternate) Composite (construc