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
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DNA vs. Protein searches
DNA vs. Protein searches
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DNA vs. Protein searches
Basic principles of db searching
Pairwise Alignment
Aligning 2 Sequences example 1
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Scoring Pairwise Alignments
Optimal alignment using scores for example 1
Pairwise Comparison of Proteins
Pairwise Comparison of Proteins
Basic principles of db searching
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Specificity and sensitivity
Two types of alignment:
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Main algorithms for database searching
The FastA software package
General view of how the fasta program works:
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Note:
Comparison programs in the FastA3 package
Comparison programs in the FastA3 package
Fasta output
Fasta output
Fasta output
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Output of FastA
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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
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Conclusions
Heuristic Vs. Rigorous
Comparison of programs
Comparison between the methods
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Tips for DB searches
Tips for DB searches
Tips for DB searches
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