Bio::Seq - Sequence object, with features $seqio = Bio::SeqIO->new ( '-format' => 'embl' , -file => 'myfile.dat'); $seqobj = $seqio->next_seq(); # features must implement Bio::SeqFeatureI @features = $seqobj->top_SeqFeatures(); # just top level @features = $seqobj->all_SeqFeatures(); # descend into sub features $seq = $seqobj->seq(); # actual sequence as a string $seqstr = $seqobj->subseq(10,50); $ann = $seqobj->annotation(); # annotation object A Seq object is a sequence with sequence features placed on them. 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 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 seqfeatures (an aggregate) with its own annotation. Although bioperl is not tied to file formats heavily, these distinctions do map to file formats sensibly and for some bioinformaticians this might help you: 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 alot of nasty ciricular references (seqfeatures can hold a reference to a sequence without the sequence holding a reference to the seqfeature). Ian Korf really helped in the design of the Seq and SeqFeature system.

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bioperl.org http://bio.perl.org/bioperl-bugs/ Email birney@sanger.ac.uk Describe contact details here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : $seq = Bio::Seq->new( -seq => 'ATGGGGGTGGTGGTACCCT', -id => 'human_id', -accession_number => 'AL000012', ); Function: Returns a new seq object from basic constructors, being a string for the sequence and strings for id and accession_number Returns : a new Bio::Seq object The primaryseq interface is the basic sequence getting and setting methods found on all sequences. These methods implement the PrimarySeq interface by delegating to the primary_seq inside the object. This means that you can use a Seq object wherever there is a PrimarySeq, and of course, you are free to use these functions anyway.

seq
Title : seq Usage : $string = $obj->seq() Function: Returns the sequence as a string of letters. The case of the letters is left up to the implementer. Suggested cases are upper case for proteins and lower case for DNA sequence (IUPAC standard), but implementations are suggested to keep an open mind about case (some users... want mixed case!) Returns : A scalar

length
Title : length Usage : $len = $seq->length() Function: Example : Returns : integer representing the length of the sequence. Args :

subseq
Title : subseq Usage : $substring = $obj->subseq(10,40); Function: returns the subseq from start to end, where the first base is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence Start cannot be larger than end but can be equal Returns : a string Args :

display_id
Title : display_id Usage : $id_string = $obj->display_id($newid); Function: returns or sets the display id, aka the common name of the Sequence object. The semantics of this is that it is the most likely string to be used as an identifier of the sequence, and likely to have "human" readability. The id is equivalent to the ID field of the GenBank/EMBL databanks and the id field of the Swissprot/sptrembl database. In fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. Bioperl does not use any embedded information in the ID field, and people are encouraged to use other mechanisms (accession field for example, or extending the sequence object) to solve this. Notice that $seq->id() maps to this function, mainly for legacy/convience issues Returns : A string Args : newid (optional)

accession_number
Title : accession_number Usage : $unique_biological_key = $obj->accession_number; Function: Returns the unique biological id for a sequence, commonly called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id for the implemetation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". Returns : A string Args : None

desc
Title : desc Usage : $seqobj->desc() Function: Sets/Gets the description of the sequnce Example : Returns : Args :

primary_id
Title : primary_id Usage : $unique_implementation_key = $obj->primary_id; Function: Returns the unique id for this object in this implementation. This allows implementations to manage their own object ids in a way the implementaiton can control clients can expect one id to map to one object. For sequences with no natural id, this method should return a stringified memory location. Also notice that this method is B<not> delegated to the internal PrimarySeq object Returns : A string Args : None

can_call_new
Title : can_call_new Usage : if( $obj->can_call_new ) { $newobj = $obj->new( %param ); } Function: can_call_new returns 1 or 0 depending on whether an implementation allows new constructor to be called. If a new constructor is allowed, then it should take the followed hashed constructor list. $myobject->new( -seq => $sequence_as_string, -display_id => $id -accession_number => $accession -moltype => 'dna', ); Example : Returns : 1 or 0 Args :

moltype
Title : moltype Usage : if( $obj->moltype eq 'dna' ) { /Do Something/ } Function: Returns the type of sequence being one of 'dna', 'rna' or 'protein'. This is case sensitive. This is not called <type> because this would cause upgrade problems from the 0.5 and earlier Seq objects. Returns : a string either 'dna','rna','protein'. NB - the object must make a call of the type - if there is no type specified it has to guess. Args : none These methods are inherited from the PrimarySeq interface and work as one expects, building new Bio::Seq objects or other information as expected. Sequence Features are not transfered to the new objects. This is possibly a mistake. Anyone who feels the urge in dealing with this is welcome to give it a go.

revcom
Title : revcom Usage : $rev = $seq->revcom() Function: Produces a new Bio::Seq object which is the reversed complement of the sequence. For protein sequences this throws an exception of "Sequence is a protein. Cannot revcom" The id is the same id as the orginal sequence, and the accession number is also indentical. If someone wants to track that this sequence has be reversed, it needs to define its own extensions To do an inplace edit of an object you can go: $seq = $seq->revcom(); This of course, causes Perl to handle the garbage collection of the old object, but it is roughly speaking as efficient as an inplace edit. Returns : A new (fresh) Bio::Seq object Args : none

trunc
Title : trunc Usage : $subseq = $myseq->trunc(10,100); Function: Provides a truncation of a sequence, Example : Returns : a fresh Bio::Seq object Args :

id
Title : id Usage : $id = $seq->id() Function: This is mapped on display_id Example : Returns : Args : These methods are specific to the Bio::Seq object, and not found on the Bio::PrimarySeq object

primary_seq
Title : primary_seq Usage : $obj->primary_seq($newval) Function: Example : Returns : value of primary_seq Args : newvalue (optional)

annotation
Title : annotation Usage : $obj->annotation($seq_obj) Function: Example : Returns : value of annotation Args : newvalue (optional)

add_SeqFeature
Title : add_SeqFeature Usage : $seq->add_SeqFeature($feat); $seq->add_SeqFeature(@feat); Function: Adds the given feature object (or each of an array of feature objects to the feature array of this sequence. The object passed is required to implement the Bio::SeqFeatureI interface. Example : Returns : TRUE on success Args : A Bio::SeqFeatureI implementing object, or an array of such objects.

top_SeqFeatures
Title : top_SeqFeatures Usage : @feat_ary = $seq->top_SeqFeatures(); Function: Returns the array of top-level features for this sequence object. Features which are not top-level are subfeatures of one or more of the returned feature objects, which means that you must traverse the subfeature arrays of each top-level feature object in order to traverse all features associated with this sequence. Use all_SeqFeatures() if you want the feature tree flattened into one single array. Example : Returns : An array of Bio::SeqFeatureI implementing objects. Args :

all_SeqFeatures
Title : all_SeqFeatures Usage : @feat_ary = $seq->all_SeqFeatures(); Function: Returns the tree of feature objects attached to this sequence object flattened into one single array. Top-level features will still contain their subfeature-arrays, which means that you will encounter subfeatures twice if you traverse the subfeature tree of the returned objects. Use top_SeqFeatures() if you want the array to contain only the top-level features. Example : Returns : An array of Bio::SeqFeatureI implementing objects. Args :

feature_count
Title : feature_count Usage : $seq->feature_count() Function: Return the number of SeqFeatures attached to a sequence Example : Returns : number of SeqFeatures Args : none

species
Title : species Usage : Function: Gets or sets the species Example : $species = $self->species(); Returns : Bio::Species object Args : Bio::Species object or none;