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BioPerl

Explore BioPerl, a powerful tool for bioinformatics that combines the flexibility of Perl with specialized modules for sequence manipulation and database access. This guide covers the advantages of using BioPerl, its object-oriented approach, availability of resources, and example scripts for sequence conversion, database retrieval, and alignment analysis. Access tutorials, project updates, and essential "How To" files to enhance your bioinformatics workflow. Visit the main source at [bioperl.org](http://bioperl.org/) for more information.

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BioPerl

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  1. BioPerl Ketan Mane IV-Lab @ SLIS, IU

  2. BioPerl • Perl and now BioPerl -- Why ??? • Availability • Advantages for Bioinformatics

  3. BioPerl • Perl – Scripting language • Powerful text parser • Includes set of regular expression & matching tools • Good string manipulation tool • Portable to web using CGI scripts

  4. BioPerl • BioPerl = Bio + Perl • Mainly object-oriented approach • Bioinformatics specific perl-modules available Sequence Manipulation Compatibility towards different database & formats Parse results from molecular biology programs

  5. BioPerl • Main url source: • http://bioperl.org/ • Includes information on: • Projects. • Tutorials. • …. Tons of other related information • Bioperl releases are also mirrored by the Comprehensive Perl Archive Network (CPAN). ...

  6. Doc/ "How To" files and the FAQ as XML Examples/Includes simple helpful scripts Bio/BioPerl modules Scripts/BioPerl reusable scripts t/Perl built-in tests Contributed/Contributed scripts not necessarily integrated into BioPerl data/Data files used for the tests BioPerl • Directory Structure BioPerl

  7. BioPerl • Sequence Manipulation • Module Bio::SeqIO • Input = Sequence, File-format (eg: FASTA) • Sample program for file format conversion: use Bio::SeqIO; $in = Bio::SeqIO->new(-file => "inputfilename", -format => 'Fasta'); $out = Bio::SeqIO->new(-file => ">outputfilename", -format => 'EMBL'); while ( my $seq = $in->next_seq() ) { $out->write_seq($seq); }

  8. BioPerl • Sequence Manipulation: • To acquire basic sequence statistics – • molecular weights • residue • codon frequencies Modules • SeqStats • SeqWord

  9. BioPerl • Database Access: • Supports sequence data retrieval from different databases: Genbank, RefSeq, Swissprot, EMBL etc.. • Sample program $gb = new Bio::DB::GenBank(); $seq1 = $gb->get_Seq_by_id('MUSIGHBA1'); $seq2 = $gb->get_Seq_by_acc('AF303112');

  10. BioPerl • Sequence Similarity Operations: • Availability of Sequence Alignment Programs • Local alignment program: Smith Waterman • Module : Bio::Tools::pSW • Sample Code: $factory = new Bio::Tools::pSW( '-matrix' => 'BLOSUM62', '-gap' => 12, '-ext' => 2);

  11. BioPerl • Parse information from mol. biology programs • Eg: Blast • Remote execution of BLAST programs with RemoteBlast.pm bioperl module • From blast report, the parse able information includes hit count, best local sequence and their scores and other … • SearchIO.pm – robust module, so preferred over Search.pm

  12. BioPerl • Thanks !!!

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