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BioPerl

BioPerl. cpan. Open a terminal and type / bin/su - start "cpan", accept all defaults install Bio:: Graphics. use Bio::Seq; use Bio::SeqIO; # create a sequence object of some DNA my $seq = Bio::Seq->new( -id => 'testseq', -seq => 'CATGTAGATAG');

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BioPerl

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  1. BioPerl

  2. cpan Open a terminal and type /bin/su - start "cpan", accept all defaults install Bio::Graphics

  3. use Bio::Seq; use Bio::SeqIO; # create a sequence object of some DNA my $seq = Bio::Seq->new( -id => 'testseq', -seq => 'CATGTAGATAG'); # print out some details about it print "seq is ", $seq->length, " bases long\n"; print "revcom seq is ", $seq->revcom->seq, "\n"; # write it to a file in Fasta format my $out = Bio::SeqIO->new( -file => '>testseq.fsa', -format => 'Fasta'); $out->write_seq($seq);

  4. http://www.bioperl.org “Bioperl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.” • Core package provides the main parsers, this is the basic package and it's required by all the other packages • Run package provides wrappers for executing some 60 common bioinformatics applications • BioPerl db package is a subproject to store sequence and annotation data in a BioSQL relational database • Network package parses and analyzes protein-protein interaction data

  5. Open Bioinformatics Foundation “.. a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.” • BioDAS - XML Infrastructure for exchanging genome annotations • BioJava - Java toolkit • BioMOBY- Data and application execution through web services • BioPerl- Perl toolkit • BioPipe - Pipelines and workflow project for creating bioinformatics protocol • BioPython - Python toolkit • BioRuby - Ruby toolkit • BioSQL - RDBMS Database schema for storing sequences, annotations, taxa data. • OBDA - a standard for sequence data access locally, remotely, and via RDBMS • EMBOSS- Sequence analysis toolkit.

  6. Open Bioinformatics Foundation “.. a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.” • BioDAS - XML Infrastructure for exchanging genome annotations • BioJava - Java toolkit • BioMOBY - Data and application execution through web services • BioPerl - Perl toolkit • BioPipe - Pipelines and workflow project for creating bioinformatics protocol • BioPython - Python toolkit • BioRuby - Ruby toolkit • BioSQL - RDBMS Database schema for storing sequences, annotations, taxa data. • OBDA - a standard for sequence data access locally, remotely, and via RDBMS • EMBOSS - Sequence analysis toolkit.

  7. BioPerl Sequence objects • Bio::Seq - Sequence object, with features • Default sequence object • Bio::PrimarySeq - Bioperl lightweight Sequence Object • CPU and memory efficient • Bio::Seq::RichSeq - Module implementing a sequence created from a rich sequence database entry • Sequences obtained from a.o. the EMBL database • Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as files in /tmp • Sequences > 100MBases

  8. Sequence and annotation schematic

  9. Incomplete list of topics covered by BioPerl: • Accessing sequence data from local and remote databases • Manipulating sequences • Translating • Obtaining basic sequence statistics (SeqStats,SeqWord) • Identifying restriction enzyme sites (Bio::Restriction) • Identifying amino acid cleavage sites (Sigcleave) • Running BLAST • Parsing BLAST and FASTA • Searching for genes and other structures on genomic DNA (Genscan, Sim4, Grail, Genemark, ESTScan, MZEF, EPCR) • Aligning 2 sequences • Aligning multiple sequences (Clustalw.pm, TCoffee.pm) • Manipulating clusters of sequences (Cluster, ClusterIO) • Representing sequence annotations • Using 3D structure objects and reading PDB files (StructureI, Structure::IO) • Tree objects and phylogenetic trees (Tree::Tree, TreeIO, PAML) • Bibliographic objects for querying bibliographic databases (Biblio) • Graphics objects for representing sequence objects as images (Graphics) • Sequence manipulation using the Bioperl EMBOSS and PISE interfaces

  10. Exercises At: http://bioperl.org/wiki/HOWTO:Graphics Try to run the: “A Better Version of the Feature Renderer” script. Modify the script to accept an accession number instead of a filename and retrieve the corresponding sequence from the EMBL database. Test with accession number: J02933 Hint: “Bio::DB::EMBL”, where is the database located? Create a BioPerl sequence object from the example1.fasta and add the ORF starting at position 11 as a feature. Display the resulting sequence object using the feature renderer script.

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