BioPerl is an active open source software project supported by the Open Bioinformatics Foundation. BioPerl is a product of community effort to produce Perl code which is useful in biology. BioPerl is a collection of Perl modules It has played an integral role in the Human Genome Project

1. Bioperl Modules
Nixon Mendez
Department of Bioinformatics

2. • BioPerl is an active open source software project supported by
the Open Bioinformatics Foundation.
• BioPerl is a product of community effort to produce Perl code which is
useful in biology.
• BioPerl is a collection of Perl modules
• It has played an integral role in the Human Genome Project
• Sequence objects
• Alignment objects
• Database searching objects
• They interact with each other
BioPerl

3. • Object Oriented
• Modules and Objects
• Flexible and Simple
• Deals with Biological Data
• Objects are created by Modules
• Objects are the container of data
Bioperl

4. Bio::Seq Module

5. • It is central Module
• Using Bio::Seq module we can create Bio::Seq object
Flavours of Seq objects
- Bio::PrimarySeq
- Bio::SeqFeature
- Bio::Seq
Bio::Seq

6. Example 1:
use Bio::Seq;
$seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt",
-display_id => "#12345",
-desc => "example 1",
-alphabet => "dna" );
print $seq_obj->seq();
Creating a sequence and an Object

7. Bio::SeqIO Module

8. • Handler for SeqIO Formats
• Used for biological file handles
• Read or Write sequences
• Supported formats include fasta, genbank, embl, swiss
(SwissProt), Entrez Gene and tracefile formats such as abi (ABI)
and scf. quence objects
Bio::SeqIO

9. Example 2:
use Bio::SeqIO;
$seqio_obj = Bio::SeqIO->new(-file => '>sequence.fasta', -format
=> 'fasta' );
Writing a sequence to a file

10. Example 3:
use Bio::Seq;
use Bio::SeqIO;
$seq_obj = Bio::Seq->new(-seq =>
"aaaatgggggggggggccccgtt",
-display_id => "#12345",
-desc => "example 1",
-alphabet => "dna" );
$seqio_obj = Bio::SeqIO->new(-file => '>sequence.fasta', -
format => 'fasta' );
$seqio_obj->write_seq($seq_obj);
Writing a sequence to a file

11. Example 4:
use Bio::SeqIO;
$seqio_obj = Bio::SeqIO->new(-file => "sequence.fasta", -format
=> "fasta" );
$seq_obj = $seqio_obj->next_seq;
print $seq_obj->seq,"n";
Retrieving a sequence from a file

12. Example 5:
use Bio::SeqIO;
$seqio_obj = Bio::SeqIO->new(-file => "sequence.fasta", -format
=> "fasta" );
while ($seq_obj = $seqio_obj->next_seq)
{
print $seq_obj->seq,"n";
}
Retrieving multiple sequence from a
file

13. THANK YOU