ASSIGNMENT 2 cont.
		Self study at S - star			i.e.  Comparative Genomics			Page 8
	Pro and Con ? Pros: - Very fast for alignment of genomes of different strains of the same species or genome of similar species. - Can handle long insertions and deletions - Can detect reverses, SNPs, repeats, and tendem repeats ? Con: - Speed suffer significantly for less similar sequences - Minimum MUM length needs to be set lower - Many more runs of Smith – Waterman in Step 3 Another Genome – Scale Alignment Method: WABA ? WJ Kent, AM Zahler, 2000, Genome Research ? Three passes - Identify homologous regions - Align in detail overlapping 2000 x 5000 base regions - Join the overlapping alignment ? Aligned 8 million bases of Caenorhaditis briggsae against the entired 97 million bases of Caenorhaditis elegans genome. - Overall similarity: 59 % sequence identity ? Run time on a Pentium III 450 mHz - First pass: 20 hrs. O (MN) - Second pass: 11 days. O (min {M,N}) - Third pass: 15 min. O (min {M,N}) Other Research Areas in Comparative Genomics ? Using genome comparison for exon prediction and regulatory region prediction ? Building phylogenetic tree based on genome comparison ? Visualization of genome alignment ? And more… Summary ? Comparative genomics is a very powerful study organism diversity, evolution, gene function, and etc. ? Think genome scale. ? Because they are new, many techniques need to be further validated. Be critical – always question the assumptions.