Beginning Perl for Bioinformatics

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W

 W (watch) debugger command

 w (window) command , 2nd

 warn function

 warnings (-w flag)

 warnings pragma

 variables, finding errors in

 web programming

web sites

 ActiveState (ActivePerl)

 bioinformatics, government-sponsored

 Bioperl modules

BLAST

 Pennsylvania State University

for this book

 protein sequence file

 CPAN , 2nd

 Ensembl, using Bioperl modules

 European Bioinformatics Institute (EBI)

 European Molecular Biology Laboratory (EMBL)

 FEATURES table

 GenBank

 Linux

 MacPerl web page

National Center for Biotechnology Information (NCBI)

 BLAST program

Perl

 online documentation

 PROSITE, protein motif information

 Protein Data Bank (PDB) , 2nd

 public database servers

 restriction enzymes

 WU-BLAST program

 while loops , 2nd

 counter initialization and increment

 global "/g" string match in

 global searches in

 if statement within, formatting

 testing with global regular expression

whitespace

 metasymbols, matching with

 in Perl programs , 2nd

 regular expressions, matching in

 removing , 2nd

wildcards

 in regular expressions

 regular expressions, comparison to

 window (w) command , 2nd

Windows systems

 filesystem

 finding Perl, already installed

 installing Perl on

 running Perl programs

 specifying input files on command line

 text editors

 Wisconsin package (GCG DNA sequence file format)

 write function , 2nd

writing

 to files

 formatted sequence data

output

 printf function

 subroutines

 WU-BLAST program

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