Multiple Sequence Alignment
•Multiple sequence alignment is probably the single-
most important bioinformatics tools.
•Many applications require accurate MSAs
•PSIBLAST
•Family and domain classification
•Pattern identification
•Structure prediction
• secondary structure
• fold recognition
•Phylogeny
•Full-genome alignments in browsers
Conservation Patterns
•Cys pairs -disulfide bonds
•His, Ser -catalytic sites
•Cys, His -metal binding sites
•Gly, Pro -ends of 2° structure elements, turns
•Lys, Arg, Asp, Glu - ligand binding
•Lys/Arg-Asp/Glu pairs - salt bridges
•Leu -coiled coils, leucine zippers
•Motifs, secondary structure, indels
