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

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

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    Shaher Bano Mirza
    106 views13 pages
    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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    Bio Perl

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    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.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    106 views13 pages

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

    Uploaded by

    Shaher Bano Mirza
    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.

    Copyright:

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    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    of 13

    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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    $Questions???

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