Bioperl Modules Nixon Mendez

Department of Bioinformatics

• 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

• Object Oriented

• Modules and Objects

• Flexible and Simple

• Deals with Biological Data

• Objects are created by Modules

• Objects are the container of data

Bioperl

Bio::Seq Module

• 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

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

Bio::SeqIO Module

• 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

Example 2:

use Bio::SeqIO;

$seqio_obj = Bio::SeqIO->new(-file => '>sequence.fasta', -format => 'fasta' );

Writing a sequence to a file

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

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

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

THANK YOU