sequence analysis alignments dot-plots scoring scheme substitution matrices search algorithms...

Sequence Analysis

• Alignments• dot-plots• scoring scheme

• Substitution matrices• Search algorithms (BLAST)

Why Compare Sequences?

Why Compare Sequences?

Why Compare Sequences?

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

Sequence Comparisons

• Homology• similarity due to a common ancestor• no degrees of homology

• Paralogy

• Orthology

Homework: Define para/ ortholog

Sequence Comparisons

Sequence Comparisons

Sequence Comparisons

Sequence Comparisons

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?

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?

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

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

Uncertainty in Alignments

S O U T H A F R I C A

S O U T H - - R I K A N

substitution

gaps

Gaps, Insertions, Deletions (Indels) & Substitutions

Global vs. Local Alignment

Global vs. Local Alignment

End-to-end

Global vs. Local Alignment

End-to-end

Not aligned

Homework: Define

Global vs. Local Alignment

End-to-end

Not aligned

Homework: When do you use which?

Dot Plots

Dot-plot of a sequence against itself

Homework: What do palindromes looklike in a dot-plot?

More dot plot examples

Internal Repeats Insertion/ Deletion Divergence

Dynamic Programming

Dynamic Programming

Dynamic Programming

Dynamic Programming

Dynamic Programming

Note the Repeats

Note the Repeats

Dynamic Programming

Repeats

Dynamic Programming

Repeats

Dynamic Programming

Repeats

Repeats

Which Alignment is Best?

www.wellesley.edu/CS/courses/CS-BiSc303/slides/alignment.pdf

Which Alignment is Best?

www.wellesley.edu/CS/courses/CS-BiSc303/slides/alignment.pdf