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BioPerl

BioPerl. Ketan Mane IV-Lab @ SLIS, IU. BioPerl. Perl and now BioPerl -- Why ??? Availability Advantages for Bioinformatics. BioPerl. Perl – Scripting language Powerful text parser Includes set of regular expression & matching tools Good string manipulation tool

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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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