Genome alignment Usman Roshan. Applications Genome sequencing on the rise Whole genome comparison provides a deeper understanding of biology – Evolutionary.

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Presentation transcript:

Genome alignment Usman Roshan

Applications Genome sequencing on the rise Whole genome comparison provides a deeper understanding of biology – Evolutionary history – Non-coding regions – Variant detection

Methods General two-fold approach 1. Find high scoring segments between pair of genomes. – Similar to BLAST like k-mer search using hash- tables – Also done with suffix tree – Similar to short read mapping strategies 2. Perform constrained alignment between high scoring segments

Simple genome alignment Find high scoring segments with hash tables Line up high scoring segments and find longest increasing subsequence (like in MUMmer) Align between the segments Output full genome alignment

Programs and experimental comparison Alignathon