Sequence Analysis Alan Christoffels alan@sanbi.ac.za.

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Presentation transcript:

Sequence Analysis Alan Christoffels alan@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?? 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 gap S O U T H A F R I C A S O U T - A F R I C A

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 gaps

End-to-end Not aligned

Why do we want to compare sequences?? Predict functions of unknown sequences; find gene families

Why do we want to compare sequences?? What is underlying hypothesis when you predict a function by comparing two sequences ????? Predict functions of unknown sequences; find gene families

Why do we want to compare sequences?? Predict functions of unknown sequences; find gene families

Why do we want to compare sequences?? Predict functions of unknown sequences; find gene families Positions not critical to function can mutate randomly!!!!!

Why do we want to compare sequences?? Predict functions of unknown sequences; find gene families Find an example where the above is not necessarily true

Sequence Comparisons similarity due to a common ancestor Homology similarity due to a common ancestor no degrees of homology Predict functions of unknown sequences; find gene families

Sequence Comparisons Predict functions of unknown sequences; find gene families

Sequence Comparisons Predict functions of unknown sequences; find gene families

Sequence Comparisons Predict functions of unknown sequences; find gene families

Sequence Comparisons Predict functions of unknown sequences; find gene families

Sequence Comparisons Dot-plots Predict functions of unknown sequences; find gene families

Dot - plots One sequence compared to another. Identify regions of similarity

Dot - plots One sequence compared to another. Identify regions of similarity

One sequence compared to another. Identify regions of similarity

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

Scoring Path