Bio::LiveSeq::Mutation - Mutation event descriptor class # full descrition of a point mutation $mutation1a = Bio::LiveSeq::Mutation->new ( -seq => 'A', -seqori => 'T', -pos => 100, -len => 1 # optional, defaults to length(seq) ); # minimal information for a point mutation $mutation1b = Bio::LiveSeq::Mutation->new ( -seq => 'A', -pos => 100 ); # insertion $mutation2 = Bio::LiveSeq::Mutation->new ( -seq => 'ATT', -pos => 100, -len => 0 ); # deletion $mutation3 = Bio::LiveSeq::Mutation->new ( -seq => '', # optional -seqori => 'TTG', # optional -pos => 100 -len => 3 ); # complex $mutation4 = Bio::LiveSeq::Mutation->new ( -seq => 'CC', -seqori => 'TTG', # optional -pos => 100 -len => 3 ); This class describes a local mutation event using minimalistic description. It is not necessary to know anything about the original sequence. You need to give the changed sequence, the position of the mutation in the (unidentified) reference sequence, and the length of the affected subsequence in the reference sequence. If the original allele sequence is given, the objects applying the mutation into the reference sequence (e.g. the Bio::LiveSeq::Mutator manpage) might check for its validity.

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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@bio.perl.org http://bio.perl.org/bioperl-bugs/ Email: heikki@ebi.ac.uk Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

seq
Title : seq Usage : $obj->seq(); Function: Sets and returns the mutated sequence. No checking is done to validate the symbols. Example : Returns : string Args : integer

seqori
Title : seqori Usage : $obj->seqori(); Function: Sets and returns the original subsequence in the reference sequence. No checking is done to validate the symbols. Optional value. Example : Returns : string Args : string

pos
Title : pos Usage : $obj->pos(); Function: Sets and returns the position of the first element in the sequence. Example : Returns : string Args : integer

len
Title : len Usage : $obj->len(); Function: Sets and returns the len of the affected original allele sequence. If value is not set, defaults to the lenght of the mutated sequence (seq). Example : Returns : string Args : string

label
Title : label Usage : $obj->label(); Function: Sets and returns the label of the affected original allele location. Label is a stable identifier whereas location can be changed by mutations. Label comes from l<Bio::LiveSeq::Gene>. Example : Returns : string Args : string

transpos
Title : transpos Usage : $obj->transpos(); Function: Sets and returns the transcript position of the mutation. Set when associated with a reference sequence. Value depends on reference molecule and the co-ordinate system used. Example : Returns : string Args : integer

issue
Title : issue Usage : $obj->issue(); Function: Sets and returns the position of the mutation in an array of mutations to be issued. Set after the validity of the mutation has been confirmed. Example : Returns : string Args : integer

prelabel
Title : prelabel Usage : $obj->prelabel(); Function: Sets and returns the prelabel of the affected original allele location. Prelabel is a stable identifier whereas location can be changed by mutations. Prelabel comes from l<Bio::LiveSeq::Gene>. Example : Returns : string Args : string

postlabel
Title : postlabel Usage : $obj->postlabel(); Function: Sets and returns the postlabel of the affected original allele location. Postlabel is a stable identifier whereas location can be changed by mutations. Postlabel comes from l<Bio::LiveSeq::Gene>. Example : Returns : string Args : string

lastlabel
Title : lastlabel Usage : $obj->lastlabel(); Function: Sets and returns the lastlabel of the affected original allele location. Lastlabel is a stable identifier whereas location can be changed by mutations. Lastlabel comes from l<Bio::LiveSeq::Gene>. Example : Returns : string Args : string