BIO-PERL

S B Mirza 1314
Bioinformatics 7th Semester (a.n)
Snk.mirza@gmail.com
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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