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Bio-Perl: S B Mirza 1314 Bioinformatics 7 Semester (A.n)

This document discusses BioPerl, which is a Perl module that extends the functionality of the Perl programming language for bioinformatics applications. BioPerl allows Perl scripts to access sequence data from databases, transform sequence file formats, retrieve information from sequences, perform sequence searches and alignments, and identify genes and other biological structures. It was started in 1995 by scientists who were tired of rewriting code for tasks like BLAST searches. Key features of BioPerl include accessing online sequence databases, changing between common file formats like FASTA and SwissProt, and obtaining metadata from sequence objects.

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Shaher Bano Mirza
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163 views13 pages

Bio-Perl: S B Mirza 1314 Bioinformatics 7 Semester (A.n)

This document discusses BioPerl, which is a Perl module that extends the functionality of the Perl programming language for bioinformatics applications. BioPerl allows Perl scripts to access sequence data from databases, transform sequence file formats, retrieve information from sequences, perform sequence searches and alignments, and identify genes and other biological structures. It was started in 1995 by scientists who were tired of rewriting code for tasks like BLAST searches. Key features of BioPerl include accessing online sequence databases, changing between common file formats like FASTA and SwissProt, and obtaining metadata from sequence objects.

Uploaded by

Shaher Bano Mirza
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PPTX, PDF, TXT or read online on Scribd
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BIO-PERL

S B Mirza 1314
Bioinformatics 7th Semester (a.n)
[email protected]
PERL(Practical Extraction and Report Language)

 PERL is written by Larry Wall,

 BIO-PERL a language extension of Perl by


including a Module (Library)

23/12/2010 S B Mirza 1314 (GCUF) BioPERL


Bioperl Project

 Itis an international association of developers of open source


Perl tools for bioinformatics, genomics and life science
research
 Started in 1995 by a group of scientists tired of rewriting
BLAST and sequence parsers for various formats
 Version 0.7 was released in 2000
 Bioperl 1.0 was released in 2002
 A paper about bioperl was published in October 2002 (Satjich
et al., 2002. The bioperl toolkit: perl modules for the life sciences.
Genome Research 12: 1611-1618.)
 Current stable release 1.6.0 was made available in January
2009

23/12/2010 S B Mirza 1314 (GCUF) BioPERL


Bioperl Modules

Perl Modules Perls script input

Perl Interpreter

output

Bioperl and Perl

23/12/2010 S B Mirza 1314 (GCUF) BioPERL /


Why bioperl for bioinformatics?

 Perl is good at file manipulation and text processing,


which make up a large part of the routine tasks in
bioinformatics.
 Perl language, documentation and many Perl packages are
freely available.
 Perl is easy to get started in, to write small and medium-
sized programs.
 Source code available (Contributed by many)

23/12/2010 S B Mirza 1314 (GCUF) BioPERL


What can Bio Perl Do?
 Accessing sequence data from local and remote
databases
 Transforming formats of database/ file records
 Getting information from sequences
 Searching for similar sequences
 Creating and manipulating sequence alignments
 Searching for genes and other structures on
genomic DNA
 Developing machine readable sequence
annotations

23/12/2010 S B Mirza 1314 (GCUF) BioPERL


Accessing Transforming
Sequence Data formats
currently supports Changing popular
on-line databases formats
 genbank .  FASTA
 RefSeq,  EMBL
 Swissprot  SwissProt
 EMBL .  etc
etc

23/12/2010 S B Mirza 1314 (GCUF) BioPERL


Information from sequences
 $seqobj->display_id();
 $seqobj->seq();
 $seqobj->subseq(5,10);
 $seqobj->accession_
 $seqobj->alphabet();
 $seqobj->primary_

23/12/2010 S B Mirza 1314 (GCUF) BioPERL


Advantages:
• Powerful: You can program a complicated task
with very few lines of code. It often takes less
than an hour to write a Perl script
• Advanced support for regular expressions (string
matching operations). This is especially useful for
text file parsing.
• Easy access to system commands from within Perl
• Support for web-based applications through CGI
interface.

23/12/2010 S B Mirza 1314 (GCUF) BioPERL


Disadvantages:
◦ Code is very concise and usually
difficult to read
◦ Slow for computationally intensive
tasks.
◦ Little control over systems resources.
◦ Not very transparent: Many trivial
tasks like initialization of variables are
done automatically, but you don’t know
exactly how

23/12/2010 S B Mirza 1314 (GCUF) BioPERL


The first program
use Bio::Perl;
# this script will only work if you have an
internet connection on the
# computer you're using, the databases you can
get sequences from
# are 'swiss', 'genbank', 'genpept', 'embl', and
'refseq‘

$seq_object =get_sequence('swiss',"ROA1_HUMAN");
write_sequence(">roa1.fasta",'fasta',$seq_object);
These files are cited here on my
website

For document file


http://www.scribd.com/doc/46698548/bioperl

For ppt file


http://www.scribd.com/doc/46698552/Bio-
Perl
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