18.417 Lecture 5

Announcements

Advanced Alignments

Dynamic Programming Review

Dynamic Programming Variations

BLAST Review

Blast topics

Advanced Alignments

Sequence Profiles

PSI Blast

Advanced Alignments

FASTA overview

FASTA diagonal finding

FASTA Implementation

Keeping best regions

Keeping best diagonal

Bounded dynamic programming

FASTA summary

Advanced Alignments

Pre-processing and data structures

Substring searching

Suffix Tree

Using suffix trees: Operations

Suffix tree running times

Suffix Tree Construction

Suffix Tree Walk

Linear Time Construction

Bounded Depth Construction

Suffixes for DNA sequences

Looking closely at representation

Advanced Alignments

Gibbs sampling

Problem Illustration

EM: Expectation Maximization

Implementation

Advanced Alignments

HMMs

Advanced Alignments

Further Reading