Pairwise Sequence Alignment

based on global alignment of closely related proteins

to compare divergent proteins compute

Dayhoff Model

short alignment, highly similar

most effective in finding potential similarities

detect known member of protein family

longer weaker local alignment

entire length of sequence

best for highly similar of sequence similar length

region of greater similarity

best for sequence that share some similiraty or different length

FASTA format

accession number

nucleotide --> nucleotide

protein --> protein

translated nucleotide --> protein

protein --> translated nucleotide

translated nucleotide --> translated nucleotide

protein sequence database

nucleotide sequence database

gene duplication

common ancestor

quantitative inference

G + Ln

opening

extension