SequenceAlignment-Application-Lirq.pptVIP

– the foundation of bioinformatics analysis 李瑞强 lirq@ Beijing Genomics Institute 2006-03-17 Types of Alignment - Algorithm Dot Plots Dynamic programing (blast, fasta) Global - Needelman-Wunsch Local - Smith-Waterman Profile based (HMM, Psi-blast) Structure based - Object DNA ?? DNA DNA ?? Protein Protein ?? Protein Protein ?? Structure Structure ?? Structure Dynamic programing in equation form Align sequence x and y. F is the DP matrix; s is the substitution matrix; d is the linear gap penalty. DP in equation form A simple example A simple example A simple example A simpl