Sequence Analysis Alignments dot-plots scoring scheme Substitution matrices Search algorithms (BLAST)
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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
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