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BioPerl - documentation

BioPerl - documentation. Bioperl tutorial http://www.bioperl.org/Core/Latest/bptutorial.html Mastering Perl for Bioinformatics: Introduction to Bioperl http://www.oreilly.com/catalog/mperlbio/chapter/ch09.pdf Bioperl documentation http://www.bioperl.org/Core/Latest/modules.html

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BioPerl - documentation

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  1. BioPerl - documentation • Bioperl tutorial http://www.bioperl.org/Core/Latest/bptutorial.html • Mastering Perl for Bioinformatics: Introduction to Bioperl http://www.oreilly.com/catalog/mperlbio/chapter/ch09.pdf • Bioperl documentation http://www.bioperl.org/Core/Latest/modules.html • Modules listing. • http://doc.bioperl.org/releases/bioperl-1.0.1/ • Unix help: man and perldoc. • http://www.pasteur.fr/recherche/unites/sis/formation/bioperl/

  2. Bio::Seq class structure

  3. Building Sequence Bio::Seq de novo:  use Bio::Seq; my $seq1 = Bio::Seq->new ( -seq => 'ATGAGTAGTAGTAAAGGTA', -id => 'my seq', -desc => 'this is a new Seq'); from a file:  use Bio::SeqIO; my $seqin = Bio::SeqIO->new ( -file => 'seq.fasta', -format => 'fasta'); my $seq3 = $seqin->next_seq(); my $seqin2 = Bio::SeqIO->newFh ( -file => 'seq.fasta', -format => 'fasta'); my $seq4 = <$seqin2>; my $seqin3 = Bio::SeqIO->newFh ( -file => 'golden sp:TAUD_ECOLI |', -format => 'swiss'); my $seq5 = <$seqin3>;

  4. Building Sequence Bio::Seq by fetching an entry from a remote database:  use Bio::DB::SwissProt; my $banque = new Bio::DB::SwissProt; my $seq6 = $banque->get_Seq_by_id('KPY1_ECOLI'); by fetching an entry from a bioperl indexed local database:  use Bio::Index::Swissprot; my $inx = Bio::Index::Swissprot->new( -filename => 'small_swiss.inx'); my $seq7 = $inx->fetch('MALK_ECOLI'); $seqobj->seq;

  5. Relation of a SwissProt entry and the corresponding Bio::Seq object components

  6. analysis tools Bio::Seq # sequence as string $seqobj->subseq(10,40); # sub-sequence as string $seqobj->trunc(10,100); # sub-sequence as fresh Bio::PrimarySeq $seqobj->translate;

  7. statistical tools Bio::Tools::SeqStats $seq_stats = Bio::Tools::SeqStats-> new(-seq=>$seqobj); $seq_stats->count_monomers(); $seq_stats->count_codons(); $weight = $seq_stats->get_mol_wt($seqobj);

  8. An universal converter with SeqIO use Bio::SeqIO; my $in = Bio::SeqIO->new(-file => "inputfilename" , '-format' => 'Fasta'); my $out = Bio::SeqIO->new(-file => ">outputfilename" , '-format' => 'EMBL'); my $seq = $in->next_seq() ; $out->write_seq($seq); • Similarly, format conversions of alignment formats using AlignIO, e.g. clustalw, fasta, phylip, Pfam, msf, bl2seq, meme.

  9. Align Classes diagram!!!

  10. Run Clustalw and print the result on standard output in Phylip format. use Bio::Tools::Run::Alignment::Clustalw; use Bio::AlignIO; my $inputfilename = $ARGV[0]; my $outform = $ARGV[1]; my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM'); my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params); my $aln = $factory->align($inputfilename); my $out = Bio::AlignIO->new ( -fh => \*STDOUT, -format => $outform ); $out->write_aln($aln);

  11. Blast search StandAloneBlast run use Bio::SeqIO; use Bio::Tools::Run::StandAloneBlast; my $Seq_in = Bio::SeqIO->new (-file => $query_file.faa, -format => 'fasta'); my $query = $Seq_in->next_seq(); my $factory = Bio::Tools::Run::StandAloneBlast->new('program' => 'blastp', 'database' => 'swissprot' ); $factory->e(1.0); # Setting parameters $factory->outfile('blast.out'); # Saving output to file my $blast_report = $factory->blastall($query); # looking at the report: many results with multiple hits with multiple hsps… my $result = $blast_report->next_result; while( my $hit = $result->next_hit()) { print "\thit name: ", $hit->name(), " significance: ", $hit->significance(), "\n"; while( my $hsp = $hit->next_hsp()) { print “hsp length: ", $hsp->length(), "\n"; }}

  12. Blast search Parse Blast results on standard input my $blast_report = new Bio::SearchIO ('-format' => 'blast', '-fh' => \*STDIN ); my $result = $blast_report->next_result; Extracting alignmernts my $pattern = $ARGV[1]; my $out = Bio::AlignIO->newFh(-format => 'clustalw' ); while( my $hit = $result->next_hit()) { if ($hit->name() =~ /$pattern/i ) { while( my $hsp = $hit->next_hsp()) { my $aln = $hsp->get_aln(); $out->write_aln($aln); }}}

  13. Blast Classes diagram

  14. Extract translations from Genbank entry

  15. Extract translations from Genbank entry my $dbin = Bio::SeqIO->newFh ( -fh => STDIN, -format => $format ); my $out = Bio::SeqIO->newFh ( -fh => STDOUT, -format => 'fasta' ); while($entry = <$dbin>) { my $entryid = $entry->id(); foreach my $feat ($entry->top_SeqFeatures()) { if ($feat->primary_tag() eq 'CDS') { my $id = $feat->has_tag('gene') ? join(' ', $feat->each_tag_value('gene')) : 'no_gene'; my $acc = $feat->has_tag('protein_id') ? join(' ', $feat->each_tag_value('protein_id')) : 'no_pid'; my $featseq = Bio::PrimarySeq->new(); my $translation = $feat->has_tag('translation') ? join(' ', $feat->each_tag_value('translation')) : if ($translation eq ``) {print "can't get the correct seq of $id|$acc **\n"; next; } $featseq->seq($translation); $featseq->id("$id|$acc"); print $out $featseq; }}}

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