Sequence Analysis
• Alignments
• dot-plots
• scoring scheme
• Substitution matrices
• Search algorithms (BLAST)
What is a sequence alignment??
S O U T H A F R I C A
S O O T H A F R I C A
S O U T H A F R I C A
S O U T H A F R I K A
What is a sequence alignment??
S O U T H A F R I C A
S O O T H A F R I C A
S O U T H A F R I C A
S O U T H A F R I K A
What is a sequence alignment??
S O U T H A F R I C A
S O O T H A F R I C A
S O U T H A F R I C A
S O U T H A F R I K A
S O U T H A F R I C A
S O U T - A F R I C A
What is a sequence alignment??
S O U T H A F R I C A
S O O T H A F R I C A
S O U T H A F R I C A
S O U T H A F R I K A
S O U T H A F R I C A
S O U T - A F R I C A
gap
Uncertainty in alignments
S O - T H A F R I C A
S O O T H - F R I K A N
S - O T H A F R I C A
S O O T H - F R I K A N
Gaps, Insertions & deletions (indels) and substitutions
S O U T H A F R I C A
S O U T H - - R I K A N
substitution
gaps
Why do we want to compare sequences??
What is underlying hypothesis when you predict a function by comparing two sequences ?????
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