Lect14 Whole Genome Assembly

An Introduction to Bioinformatics Algorithms (Computational Molecular Biology)

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Unformatted text preview: Whole Genome Assembly Microarray analysis Mate Pairs • Mate-pairs allow you to merge islands (contigs) into super-contigs Super-contigs are quite large • Make clones of truly predictable length. EX: 3 sets can be used: 2Kb, 10Kb and 50Kb. The variance in these lengths should be small. • Use the mate-pairs to order and orient the contigs, and make super- contigs. Problem 3: Repeats Repeats & Chimerisms • 40-50% of the human genome is made up of repetitive elements. • Repeats can cause great problems in the assembly! • Chimerism causes a clone to be from two different parts of the genome. Can again give a completely wrong assembly Repeat detection • Lander Waterman strikes again! • The expected number of clones in a Repeat containing island is MUCH larger than in a non-repeat containing island (contig). • Thus, every contig can be marked as Unique, or non-unique. In the first step, throw away the non-unique islands. Repeat Detecting Repeat Contigs 1: Read Density • Compute the log-odds ratio of two hypotheses: • H1: The contig is from a unique region of the genome. • The contig is from a region that is repeated at least twice Detecting Chimeric reads • Chimeric reads: Reads that contain sequence from two genomic locations. • Good overlaps: G(a,b) if a,b overlap with a high score • Transitive overlap: T(a,c) if G(a,b), and G(b,c) • Find a point x across which only transitive overlaps occur. X is a point of chimerism Contig assembly • Reads are merged into contigs upto repeat boundaries. • (a,b) & (a,c) overlap, (b,c) should overlap as well. Also, – shift(a,c)=shift(a,b)+shift(b,c) • Most of the contigs are unique pieces of the genome, and end at some Repeat boundary. • Some contigs might be entirely within repeats. These must be detected Creating Super Contigs Supercontig assembly • Supercontigs are built incrementally • Initially, each contig is a supercontig. • In each round, a pair of super-contigs is merged until no more can be performed. • Create a Priority Queue with a score for every pair of ‘mergeable supercontigs’. – Score has two terms: • A reward for multiple mate-pair links • A penalty for distance between the links. Supercontig merging • Remove the top scoring pair (S 1 ,S 2 ) from the priority queue. • Merge (S 1 ,S 2 ) to form contig T. • Remove all pairs in Q containing S 1 or S 2 • Find all supercontigs W that share mate-pair links with T and insert (T,W) into the priority queue....
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This note was uploaded on 02/14/2008 for the course CSE 182 taught by Professor Bafna during the Fall '06 term at UCSD.

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Lect14 Whole Genome Assembly - Whole Genome Assembly...

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