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Using Perl for Bioinformatics
Module 2: BioPerl
Jason Stajich, jason.stajich@duke.edu
Contents
This Document
Bioperl Basics
Bioperl Semantics
Bioperl Name space
Interfaces
Sequence Analysis
Sequence Objects
Sequence Annotation
Sequence Input/Output
Sequence Databases
Bioperl database interfaces
Local databases and Index files
Remote databases
SQL databases
Sequence Analysis: Parsing and Running
Parsing Analysis
BLAST parsing
Multiple Sequence Alignment Parsing
Gene prediction parsing
Generalize Parsing of Analysis
Running Analyses
BLAST
ClustalW and TCoffee
Summary
About this document ...
Jason Eric Stajich 2001-08-05
