Bio::Map::PositionWithSequence(3) A position with a sequence.


use Bio::Map::PositionWithSequence;

my $pos = Bio::Map::PositionWithSequence->new(-map => $map,
-element => $element,
-start => 0,
-seq => 'ATGC');


Have a position with a sequence, eg. define what the binding site sequence of a certain transcription factor binding site is by modelling it as one of these objects with the -element assigned to a Bio::Map::TranscriptionFactor instance.


Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  [email protected]                  - General discussion  - About the mailing lists


Please direct usage questions or support issues to the mailing list:

[email protected]

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

AUTHOR - Sendu Bala

Email [email protected]


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : my $obj = Bio::Map::PositionWithSequence->new();
 Function: Builds a new Bio::Map::PositionWithSequence object 
 Returns : Bio::Map::PositionWithSequence
 Args    : -map      => Bio::Map::GeneMap object
           -element  => Bio::Map::Gene object
           -relative => Bio::Map::GeneRelative object
           -seq      => string, length of this string will set the length
                        of this position's range
           * If this position has no range, or if a single value can describe
             the range *
           -value => scalar             : something that describes the single
                                          point position or range of this
                                          Position, most likely an int
           * Or if this position has a range, at least two of *
           -start => int                : value of the start co-ordinate
           -end => int                  : value of the end co-ordinate
           -length => int               : length of the range


 Title   : seq
 Usage   : my $string = $obj->seq();
 Function: Get/set the sequence as a string of letters.
 Returns : scalar
 Args    : Optionally on set the new value (a string). An optional second
           argument presets the alphabet (otherwise it will be guessed).