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?

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

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 K A







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

substitution

gaps

Gaps, Insertions, Deletions (Indels) & Substitutions

Global vs. Local Alignment


End-to-end


End-to-end

Not aligned

Homework: Define


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

Note the Repeats

Note the Repeats

Dynamic Programming

Repeats

Dynamic Programming

Repeats

Repeats

Which Alignment is Best?

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

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

Documents

s o o t h f r i

s o t h

s o u t h

f r i c

n s o t h

endtoend slide

dynamic programming

para ortholog slide