斯坦福大学遗传生物信息课程lecture.pptxVIP

DNA Sequencing;DNA sequencing;Which representative of the species?;;Human population migrations;Why humans are so similar;Migration of human variation;Migration of human variation;Migration of human variation;;;;DNA Sequencing – Overview;DNA Sequencing;DNA Sequencing – vectors;Different types of vectors;DNA Sequencing – gel electrophoresis;Pyrosequencing / 454;Solexa / ABI SOLiD;Illumina / Affymetrix genotyping;1990;Human Genome Project (1990 – 2003);100 million species;What genes are on/off, when, and in which cells?;Comparison;Method to sequence longer regions;Reconstructing the Sequence (Fragment Assembly);Definition of Coverage;Repeats;;What can we do about repeats?;What can we do about repeats?;What can we do about repeats?;Sequencing and Fragment Assembly;Sequencing and Fragment Assembly;Strategies for whole-genome sequencing ;Hierarchical Sequencing;Hierarchical Sequencing Strategy;Methods of physical mapping;1. Hybridization;2. Digestion;;Whole Genome Shotgun Sequencing;Fragment Assembly(in whole-genome shotgun sequencing);Fragment Assembly;Steps to Assemble a Genome;1. Find Overlapping Reads;1. Find Overlapping Reads;;1. Find Overlapping Reads;2. Merge Reads into Contigs;2. Merge Reads into Contigs;2. Merge Reads into Contigs;2. Merge Reads into Contigs;2. Merge Reads into Contigs;2. Merge Reads into Contigs;Overlap graph after forming contigs;Repeats, errors, and contig lengths;;;;Fill gaps in supercontigs with paths of repeat contigs;4. Derive Consensus Sequence;Some Assemblers;Quality of assemblies;Quality of assemblies—mouse ;Quality of assemblies—mouse;Quality of assemblies—rat ;History of WGA;Genomes Sequenced