Sequence Analysis

Alan Christoffelsalan@sanbi.ac.za

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

What is a sequence alignment??

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S O O T H 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

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

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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

End-to-end

Not aligned

Why do we want to compare sequences??

Why do we want to compare sequences??

What is underlying hypothesis when you predict a function by comparing two sequences ?????

Why do we want to compare sequences??

Why do we want to compare sequences??

Positions not critical to function can mutate randomly!!!!!

Why do we want to compare sequences??

Find an example where the above is not necessarily true

Sequence Comparisons

• Homology

• similarity due to a common ancestor

• no degrees of homology

Sequence Comparisons

Sequence Comparisons

Sequence Comparisons

Sequence Comparisons

Sequence Comparisons

Dot-plots

Dot - plots

Dot - plots

What do palindromes look like in a dot-plot????

Scoring Path