ALIGNMENT

Alignments

Alignments

Origins of Sequence Similarity

Similarity

Mismatches

Terminal Mismatch

INDELS

Indels, cont’d

Similarity Scoring

DNA Scoring

Absurdity of Low Gap Penalty

Algorithms

Programs

BESTFIT vs GAP

Statistical Significance

Program Limitations

Protein Similarity

Single-Base Evolution

Substitution Matrices

PAM-Dayhoff

BLOSUM-Henikoff&Henikoff

BLOSUM62

BLOSUM62-2

Gaps

Alignment Statistics

“Real” Alignments

Real Alignments

Phylogeny

Cow-to-Pig

Cow-to-Pig cDNA

DNA similarity reflects polypeptide similarity

Coding vs Non-coding Regions

Third Base of Codon Hypervariable

Cow-to-Fish Protein

Cow-to-Fish DNA

Protein vs DNAAlignments