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Bio::Seq 1.4

  Date Added: September 26, 2010  |  Visits: 570

Bio::Seq

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Bio::Seq is a sequence object, with features. SYNOPSIS # This is the main sequence object in Bioperl # gets a sequence from a file $seqio = Bio::SeqIO->new( -format => embl , -file => myfile.dat); $seqobj = $seqio->next_seq(); # SeqIO can both read and write sequences; see Bio::SeqIO # for more information and examples # get from database $db = Bio::DB::GenBank->new(); $seqobj = $db->get_Seq_by_acc(X78121); # make from strings in script $seqobj = Bio::Seq->new( -display_id => my_id, -seq => $sequence_as_string); # gets sequence as a string from sequence object $seqstr = $seqobj->seq(); # actual sequence as a string $seqstr = $seqobj->subseq(10,50); # slice in biological coordinates # retrieves information from the sequence # features must implement Bio::SeqFeatureI interface @features = $seqobj->get_SeqFeatures(); # just top level foreach my $feat ( @features ) { print "Feature ",$feat->primary_tag," starts ",$feat->start," ends ", $feat->end," strand ",$feat->strand,"n"; # features retain link to underlying sequence object print "Feature sequence is ",$feat->seq->seq(),"n" } # sequences may have a species if( defined $seq->species ) { print "Sequence is from ",$species->binomial_name," [",$species->common_name,"]n"; } # annotation objects are Bio::AnnotationCollectionIs $ann = $seqobj->annotation(); # annotation object # references is one type of annotations to get. Also get # comment and dblink. Look at Bio::AnnotationCollection for # more information foreach my $ref ( $ann->get_Annotations(reference) ) { print "Reference ",$ref->title,"n"; } # you can get truncations, translations and reverse complements, these # all give back Bio::Seq objects themselves, though currently with no # features transfered my $trunc = $seqobj->trunc(100,200); my $rev = $seqobj->revcom(); # there are many options to translate - check out the docs my $trans = $seqobj->translate(); # these functions can be chained together my $trans_trunc_rev = $seqobj->trunc(100,200)->revcom->translate(); A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In Bioperl we have 3 main players that people are going to use frequently Bio::PrimarySeq - just the sequence and its names, nothing else. Bio::SeqFeatureI - a location on a sequence, potentially with a sequence and annotation. Bio::Seq - A sequence and a collection of sequence features (an aggregate) with its own annotation. Although Bioperl is not tied heavily to file formats these distinctions do map to file formats sensibly and for some bioinformaticians this might help Bio::PrimarySeq - Fasta file of a sequence Bio::SeqFeatureI - A single entry in an EMBL/GenBank/DDBJ feature table Bio::Seq - A single EMBL/GenBank/DDBJ entry By having this split we avoid a lot of nasty circular references (sequence features can hold a reference to a sequence without the sequence holding a reference to the sequence feature). See Bio::PrimarySeq and Bio::SeqFeatureI for more information. Ian Korf really helped in the design of the Seq and SeqFeature system..

Requirements: No special requirements
Platforms: Linux
Keyword: Annotation Bioseq Features Genbank Libraries Object Primaryseq Programming Reference Seq Seqfeaturei Seqio Sequence
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License: Freeware Size: 4.7 MB
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