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
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