Getting Started

From BioPerl

Contents 1 Download 2 Installation 3 Quick example 4 Beginners 5 Further reading

Download

See Getting BioPerl

Installation

See Installing BioPerl

Quick example

use Bio::Seq;
use Bio::SeqIO;
 
# create a sequence object of some DNA
my $seq = Bio::Seq->new(-id => 'testseq', -seq => 'CATGTAGATAG');
 
# print out some details about it
print "seq is ", $seq->length, " bases long\n";
print "revcom seq is ", $seq->revcom->seq, "\n";
 
# write it to a file in Fasta format 
my $out = Bio::SeqIO->new(-file => '>testseq.fsa', -format => 'Fasta');
$out->write_seq($seq);

For more information (for those familiar with Perl) see: Bio::Seq.

Beginners

• Learn how to program in Perl, see several Tutorials
  • Genome Informatics
  • PerlMonks Tutorials
  • Perl.com tutorials
  • Picking up Perl
  • Learn Perl
• Read the Beginners HOWTO
• Browse the Bioperl Tutorial
• Examine the Class Diagram if you'd like to know more about the relationships between the modules.

Further reading

• Read the other HOWTOs
• Use the Wiki Search tools to find more information on specific topics.