Bio::LocatableSeq - A Sequence object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. use Bio::LocatableSeq; my $seq = new Bio::LocatableSeq(-seq => "CAGT-GGT", -id => "seq1", -start => 1, -end => 7); # a normal sequence object $locseq->seq(); $locseq->id(); # has start,end points $locseq->start(); $locseq->end(); # inheriets off RangeI, so range operations possible

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 The locatable sequence object was developed mainly because the SimpleAlign object requires this functionality, and in the rewrite of the Sequence object we had to decide what to do with this. It is, to be honest, not well integrated with the rest of bioperl, for example, the trunc() function does not return a LocatableSeq object, as some might have thought. There are all sorts of nasty gotcha's about interactions between coordinate systems when these sort of objects are used.

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://bugzilla.bioperl.org/ The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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

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

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

get_nse
Title : get_nse Usage : Function: read-only name of form id/start-end Example : Returns : Args :

no_gap
Title : no_gaps Usage :$self->no_gaps('.') Function: Gets number of gaps in the sequence. The count excludes leading or trailing gap characters. Valid bioperl sequence characters are [A-Za-z\-\.\*]. Of these, '.' and '-' are counted as gap characters unless an optional argument specifies one of them. Returns : number of internal gaps in the sequnce. Args : a gap character (optional)

column_from_residue_number
Title : column_from_residue_number Usage : $col = $seq->column_from_residue_number($resnumber) Function: This function gives the position in the alignment (i.e. column number) of the given residue number in the sequence. For example, for the sequence Seq1/91-97 AC..DEF.GH column_from_residue_number(94) returns 5. An exception is thrown if the residue number would lie outside the length of the aligment (e.g. column_from_residue_number( "Seq2", 22 ) Returns : A column number for the position of the given residue in the given sequence (1 = first column) Args : A residue number in the whole sequence (not just that segment of it in the alignment)

location_from_column
Title : location_from_column Usage : $loc = $ali->location_from_column($column_number) Function: This function gives the residue number for a given position in the alignment (i.e. column number) of the given. Gaps complicate this process and force the output to be a L<Bio::Range> where values can be undefined. For example, for the sequence: Seq/91-97 .AC..DEF.G. location_from_column( 3 ) position 93 location_from_column( 2 ) position 92^93 location_from_column(10 ) position 97^98 location_from_column( 1 ) position undef An exact position returns a Bio::Location::Simple object where where location_type() returns 'EXACT', if a position is between bases location_type() returns 'IN-BETWEEN'. Column before the first residue returns undef. Note that if the position is after the last residue in the alignment, that there is no guarantee that the original sequence has residues after that position. An exception is thrown if the column number is not within the sequence. Returns : Bio::Location::Simple or undef Args : A column number Throws : If column is not within the sequence See Bio::Location::Simple for more.

revcom
Title : revcom Usage : $rev = $seq->revcom() Function: Produces a new Bio::LocatableSeq object which has the reversed complement of the sequence. For protein sequences this throws an exception of "Sequence is a protein. Cannot revcom" Returns : A new Bio::LocatableSeq object Args : none

trunc
Title : trunc Usage : $subseq = $myseq->trunc(10,100); Function: Provides a truncation of a sequence, Example : Returns : a fresh Bio::PrimarySeqI implementing object Args : Two integers denoting first and last columns of the sequence to be included into sub-sequence.