Perl

• Comprehensive Perl Archive Network (CPAN modules and documentation)
• Perl.com: O'Reilly's Perl resources (including Perl download for Unix)
• ActivePerl: Perl for Windows (download and documentation)
• Perl functions
• Perl Frequently Asked Questions
• Installing Perl modules (but check first - the module may already be installed) - and you'll need to specify the PREFIX when running Makefile.PL
• Genome Informatics at CSHL: Perl basics, control structures, arrays and hashes, loops and filehandles, regular expressions, modules

BioPerl

• BioPerl home
• BioPerl tutorial
• BioPerl documentation on CPAN
• BioPerl documentation on BioPerl
• BioPerl course (Pasteur Institute)
• How Perl Saved the Human Genome Project (Lincoln Stein)

General programming

• How To Become A Hacker: advice from Eric Raymond

Sample Perl scripts

• hey.pl: test Perl on your system
• rev_comp.pl: reverse and complement a fasta sequence using EMBOSS's 'revseq' command
• patscan_batch.pl: run patscan (to search for a pattern) on every sequence in a directory
• oligos.pl: extract oligos from a sequence and analyze them
• puzzle_helper.html: a web-based interface for the puzzle.cgi script using a regular expression with the Unix 'grep' command
• parse_genbank.pl: a simple GenBank nucleotide report parser using regular expressions (input and output)
• get_web_data.pl: use LWP to automate web file access
• draw_figure.pl: draw a PNG figure using the GD module (sample input and output)
• fastaToGenbank_1.pl and fastaToGenbank_2.pl: examples of sequence conversion with BioPerl (sample input and output)
• genbank_parse.pl: parse GenBank sequence features with BioPerl (sample input and output)
• manipulate_seq.pl: manipulate a sequence with BioPerl (sample input and output)
• blast_parse_0.pl: parse BLAST output files with BioPerl's SearchIO (sample input and output)
• blast_parse_1.pl: parse BLAST output files with BioPerl's BPlite (sample input and output)
• blast_parse_2.pl: parse BLAST output files with NHGRI's Blast (sample input and output)

Perl modules (documentation)

• LWP: library for WWW access in Perl
• LWP::Simple: procedural LWP interface
• CGI: creating scripts with a Web interface
• GD: generate graphics
• BioPerl's SeqIO: for sequence input/output and format conversion
• BioPerl's SearchIO: best BioPerl BLAST report parser
• BioPerl's BPlite: old BioPerl BLAST report parser
• NHGRI's BLAST: BLAST report parser

Books

• Learning Perl: "the llama book", a popular place to start
• Programming Perl: "the camel book", a popular reference
• Perl CD Bookshelf
• Beginning Perl for Bioinformatics

Other resources

• Linking to PubMed and other Entrez databases : generating URLs for queries