overview Comparative genomics overview Structural Genomics Comparative Genomics

overview Comparative genomics

overview Structural Genomics Comparative Genomics Functional genomics

overview • Pairwise alignment – Exact algorithms – Heuristic algorithms (Fast. A, Blast) • Multiple alignments – Exact algorithms – Heuristic algorithms (clustal. W) • Profile searches • Motif detection (improved multiple alignment for nucleotide sequences based on profiles)

Algorithms overview Pairwise Alignment Dynamic programming Needleman Wunsch Smith Waterman (global) (local) Chapter 1 Heuristic approaches Fast. A Blast Database searches Chapter 1

Algorithms overview Multiple Alignment Dynamic Programming Pattern recognition Heuristic Searches HMM Motif Searches Database searches Chapter 2

Introduction overview Multiple sequence alignment Features characteristic for the protein family Profile (HMM) Phylogeny Detect remote members of the family Reconstruct phylogenetic relationships

Introduction overview Multiple sequence alignment Features characteristic for the whole family How to represent the characteristic features? Profile: captures the family characteristic features • regular expression, weight matrix, HMM profile

Introduction overview • Profile: captures the family characteristic features • Used to detect remote homologs of a family • In this course emphasis on nucleotide sequences Multiple sequence alignment Unaligned sequences Construct profile Scan new sequence with the profile

Overview overview Query Sequence Unknown Blast Sequence to search for close homologs PFAM PROSITE Search p. FAM, Prosite for conserved motifs You detected homology with an annotated protein family Clustal. W Make a multiple sequence alignment HMMer, PSSM PSI-blast Generate profile or HMM Profile Search database for remote homologs