Pair-wise Sequence Comparison
• Basis for relating biological information from a
well-studied gene to a new sequence
• Many programs exist for pairwise comparison
• Some specialize in fast database searching and
get “good” alignments
– One sequence v. many thousands:
• BLAST or FASTA
• Some are much slower, but guarantee the
“optimal alignment”
– Smith-Waterman is the de facto standard
What is Optimal??
• How do we get an “optimal” alignment
• Optimal to who?
• Optimal based on scoring model:
– Substitution scoring matrix
– Insertion / deletion scoring (penalties)
• Caution: Just because it is optimal for a
given scoring scheme, doesn’t mean it is
biologically correct!!
