MIT CompBio Lecture 03 - Hashing BLAST Database Search (Fall'19)
March 16, 2021
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1:23:05Now PlayingMIT CompBio Lecture 03 - Hashing BLAST Database Search (Fall'19)
YouTube Description
as posted by the channelMIT Computational Biology: Genomes, Networks, Evolution, Health
Prof. Manolis Kellis
Full playlist with all videos in order is here
All slides from Fall 2019 are here
Outline for this lecture:
1. Global alignment vs. Local alignment
- Needleman-Wunsch and Smith-Waterman
- Varying gap penalties and algorithmic speedups
2. Linear-time exact string matching (expected)
- Karp-Rabin algorithm and semi-numerical methods
- Hash functions and randomized algorithms
3. The BLAST algorithm and inexact matching
- Hashing with neighborhood search
- Two-hit blast and hashing with combs
4. Probabilistic foundations of sequence alignment
- Mismatch penalties, BLOSUM and PAM matrices
- Statistical significance of an alignment score
5. Deterministic linear-time exact string matching
- Key insight: gather more info from each comparison
- Pre-processing, Z-algorithm, Boyer-More, KMP
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