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