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Biological Databases and Retrieval
Biological Databases and Retrieval Systems
Available Databases
Database Searching of DNA (Nucleotide Sequences)
Database Searching of Proteins (Amino Acid Sequence)
How to Perform Database-Searching
Sequence Retrieval System (SRS)
Entrez
DBGET
DNA vs. Protein Searches
Specificity and Sensitivity of the Search Tools
Main Algorithms for Database Searching
The FastA Software Package
Variants of FastA
Sketch of the FastA Algorithm (see also lecture No. 3)
Programs in the FastA3 Package
Which Program When?
FastA Output
Tips for FastA Results
BLAST - Basic Local Alignment Search Tool
Variants of BLAST
General View of How the BLAST Program Works (see also lecture No. 3):
BLAST Output
The Smith-Waterman Tool
Comparison of the Programs
Tips for DB Searches
Multiple Sequence Alignment
Why to Performing Multiple Alignments?
General View of How the Programs Work:
Choosing Sequences for Alignment
Pileup - Multiple Alignment in GCG
Displaying a Multiple Alignment in GCG
ShadyBox
ClustalW- for Multiple Alignment
Blocks Database and Tools
General View of How the Program Works
Other Uses of the Blocks Database
The Blocks Searcher Tool
The Block Maker Tool
Recommended Sites on the Web
Bibliography
About this document ...
Itshack Pe`er
1999-01-17
