1. BioPerl - documentation Bioperl tutorial http://www.bioperl.org/Core/Latest/bptutorial.htmlBioperl tutorial Mastering Perl for Bioinformatics: Introduction to Bioperl http://www.oreilly.com/catalog/mperlbio/chapter/ch09.pdfMastering Perl for Bioinformatics: Introduction to Bioperl Bioperl documentation http://www.bioperl.org/Core/Latest/modules.htmlBioperl documentation 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 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 = ; my $seqin3 = Bio::SeqIO->newFh ( -file => 'golden sp:TAUD_ECOLI |', -format => 'swiss'); my $seq5 = ; de novo: use Bio::Seq; my $seq1 = Bio::Seq->new ( -seq => 'ATGAGTAGTAGTAAAGGTA', -id => 'my seq', -desc => 'this is a new Seq');

4. Building Sequence Bio::Seq 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; 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');

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

7. 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;

8. 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);

9. 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.

11. Align Classes diagram!!!

12. 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);

13. 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"; }}

14. 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); }}} Blast search

15. Blast Classes diagram

16. Extract translations from Genbank entry

17. my $dbin = Bio::SeqIO->newFh ( -fh => STDIN, -format => $format ); my $out = Bio::SeqIO->newFh ( -fh => STDOUT, -format => 'fasta' ); while($entry = ) { 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; }}}