Table of Contents18.417 Intro to Computational Biology Lecture 4 BLAST & Database Search BLAST and Database Search More sequence - New problems Speeding up your searches BLAST and Database Search What is hashing PPT Slide Blast Algorithm Overview Breaking up the query Generating the neighborhood Looking into database Extending the seeds Statistical Significance PPT Slide BLAST and Database Search Extensions: Filtering Extensions: Two-hit blast BLAST and Database Search Substitution Matrices Amino Acids PAM matrices BLOSUM matrices Computing Substitution Matrices BLAST and Database Search Overview: Why k-mers work Pigeonhole principle Extending pigeonhole principle Pigeonhole and sequences: Worst case Random model: Average case PPT Slide Random Model: simulation PPT Slide True alignments: Looking for K-mers True alignments: Looking for K-mers Summary: Why k-mers work BLAST and Database Search Identifying exons Part I - Parameter tuning Part II - choosing a threshold Part III - Gene identification Estimating human gene number Gene content by Chromosome |
Author: Manolis Kamvysselis
Email: manoli@mit.edu Home Page: http://theory.lcs.mit.edu/~bab/01-18.417-home.html Other information: |