Database Similarity Searching

4/7/03


Click here to start


Table of Contents

Database Similarity Searching

Why search databases?

What databases are available?

What databases are available?

What is a homologous sequence?

DNA vs. Protein searches

DNA vs. Protein searches

PPT Slide

DNA vs. Protein searches

DNA vs. Protein searches

PPT Slide

DNA vs. Protein searches

Basic principles of db searching

Pairwise Alignment

Aligning 2 Sequences example 1

PPT Slide

Scoring Pairwise Alignments

Optimal alignment using scores for example 1

Pairwise Comparison of Proteins

Pairwise Comparison of Proteins

Basic principles of db searching

PPT Slide

Specificity and sensitivity

Two types of alignment:

PPT Slide

Main algorithms for database searching

The FastA software package

General view of how the fasta program works:

PPT Slide

PPT Slide

PPT Slide

PPT Slide

Note:

Comparison programs in the FastA3 package

Comparison programs in the FastA3 package

Fasta output

Fasta output

Fasta output

PPT Slide

Output of FastA

PPT Slide

Output of FastA

Output of FastA

Statistical evaluation of results

BLAST - Basic Local Alignment Search Tool

BLAST - Basic Local Alignment Search Tool

Blast method

BLAST - Basic Local Alignment Search Tool

Steps used by Blast algorithm

Steps used by Blast algorithm

Steps used by Blast algorithm

Steps used by Blast algorithm

Steps used by Blast algorithm

Steps used by Blast algorithm

Steps used by Blast algorithm

Steps used by Blast algorithm

Steps used by Blast algorithm

Blast output

Blast output

BLAST Programs

The Smith-Waterman Tools

PPT Slide

PPT Slide

Conclusions

Heuristic Vs. Rigorous

Comparison of programs

Comparison between the methods

PPT Slide

PPT Slide

PPT Slide

Tips for DB searches

Tips for DB searches

Tips for DB searches

PPT Slide

Author: weizmann

Email: shifra.ben-dor@weizmann.ac.il