Whole Genome Sequencing.ppt

Whole Genome Sequencing (Lecture for CS498-CXZ Algorithms in Bioinformatics) Sept. 13, 2005 ChengXiang Zhai Department of Computer Science University of Illinois, Urbana-Champaign Outline Practical challenges in genome sequencing Whole genome sequencing strategies Sequencing coverage (Lander-Waterman model) Overlap-Layout-Consensus approach Repeat Types Low-Complexity DNA (e.g. ATATATATACATA…) Microsatellite repeats (a1…ak)N where k ~ 3-6 (e.g. CAGCAGTAGCAGCACCAG) Transposons/retrotransposons SINE Short Interspersed Nuclear Elements (e.g., Alu: ~300 bp long, 106 copies) LINE Long Interspersed Nuclear Elements ~500 - 5,000 bp long, 200,000 copies LTR retroposons Long Terminal Repeats (~700 bp) at each end Gene Families genes duplicate then diverge Segmental duplications ~very long, very similar copies The sequencing errors, repeats, and the complexity of genomes make it necessary to use many heuristics in practice… Strategies for whole-genome sequencing Hierarchical – Clone-by-clone yeast, worm, human Break genome into many long fragments Map each long fragment onto the genome Sequence each fragment with shotgun Online version of (1) – Walking rice genome Break genome into many long fragments Start sequencing each fragment with shotgun Construct map as you go Whole Genome Shotgun fly, human, mouse, rat, fugu One large shotgun pass on the whole genome Hierarchical Sequencing vs. Whole Genome Shotgun Hierarchical Sequencing Advantages: Easy assembly Disadvantages: Build library physical map; Redundant sequencing Whole Genome Shotgun (WGS) Advantages: No mapping, no redundant sequencing Disadvantages: Difficult to assemble and resolve repeats Whole Genome Shotgun Sequencing Fragment Assembly Read Coverage Length of genomic segment: G Number of reads: N Length of each read: L Definition: Coverage C = NL/ G Enough Coverage How much coverage is enough? According to the Lander-Waterman model: