Ewan Birney

NAME

Bio::Map::Microsatellite - An object representing a Microsatellite marker.

SYNOPSIS

  $o_usat = new Bio::Map::Microsatellite
      (-name=>'Chad Super Marker 2',
       -sequence => 'gctgactgatcatatatatatatatatatatatatatatatcgcgatcgtga',
       -motif => 'at',
       -repeats => 15,
       -repeat_start_position => 11
       );

  $sequence_before_usat = $o_usat->get_leading_flank();
  $sequence_after_usat = $o_usat->get_trailing_flank();

DESCRIPTION

This object handles the notion of an Microsatellite. This microsatellite can be placed on a (linear) Map or used on its own. If this Microsatellites will be used in a mapping context (it doesn't have to, you know) it can have multiple positions in a map. For information about a Microsatellite's position in a map one must query the associate PositionI object which is accessible through the position() method.

FEEDBACK

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.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

AUTHOR - Chad Matsalla

Email bioinformatics1@dieselwurks.com

CONTRIBUTORS

Heikki Lehvaslaiho heikki@ebi.ac.uk Lincoln Stein lstein@cshl.org Jason Stajich jason@bioperl.org

APPENDIX

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

new

 Title   : new
 Usage   : $o_usat = 
 Function: Builds a new Bio::Map::Microsatellite object
 Returns : Bio::Map::Microsatellite
 Args    :
        -name    => name of this microsatellite (optional, string,
                default 'Unknown microsatellite')
        -positions => position(s) for this marker in maps[optional],
                An array reference of tuples (array refs themselves)
                Each tuple conatins a Bio::Map::MapI-inherited object and a 
                Bio::Map::PositionI-inherited obj, no default)
        -sequence => the sequence of this microsatellite (optional,
                 scalar, no default)
        -motif => the repeat motif of this microsatellite (optional,
                 scalar, no default)
        -repeats => the number of motif repeats for this microsatellite
                (optional, scalar, no default)
        -repeat_start_position => the starting position of the
                microsatellite in this sequence. The first base of the
                sequence is position "1". (optional, scalar, no default)

 Note    : Creating a Bio::Map::Microsatellite object with no position
        might be useful for microsatellite people wanting to embrace
        and extend this module. <raising hand> Me! Me! Me!
        - using repeat_start_position will trigger a mechinism to
        calculate a value for repeat_end_position. 

Bio::Map::Marker methods

position

 Title   : position
 Usage   : my $position = $mappable->position($map); OR
           $mappable->position($map,$position); OR
 Function: Get/Set the Bio::Map::PositionI for a mappable element
           in a specific Map
 Returns : Bio::Map::PositionI
 Args    : $map =Bio::Map::MapI # Map we are talking about
           $position = Bio::Map::PositionI # Position we want to set

name($new_name)

 Title   : name($new_name)
 Usage   : $o_usat->name($new_name) _or_
           my $name = $o_usat->name()
 Function: Get/Set the name for this Microsatellite
 Returns : A scalar representing the current name of this Microsatellite
 Args    : If provided, the current name of this Microsatellite
           will be set to $new_name.

motif($new_motif)

 Title   : motif($new_motif)
 Usage   : my $motif = $o_usat->motif($new_motif) _or_
        my $motif = $o_usat->motif()
 Function: Get/Set the repeat motif for this Microsatellite
 Returns : A scalar representing the current repeat motif of this
        Microsatellite.
 Args    : If provided, the current repeat motif of this Microsatellite
        will be set to $new_motif.

sequence($new_sequence)

 Title   : sequence($new_sequence)
 Usage   : my $sequence = $o_usat->sequence($new_sequence) _or_
        my $sequence = $o_usat->sequence()
 Function: Get/Set the sequence for this Microsatellite
 Returns : A scalar representing the current sequence of this
        Microsatellite.
 Args    : If provided, the current sequence of this Microsatellite
        will be set to $new_sequence.

repeats($new_repeats)

 Title   : repeats($new_repeats)
 Usage   : my $repeats = $o_usat->repeats($new_repeats) _or_
        my $repeats = $o_usat->repeats()
 Function: Get/Set the repeat repeats for this Microsatellite
 Returns : A scalar representing the current number of repeats of this
        Microsatellite.
 Args    : If provided, the current number of repeats of this
        Microsatellite will be set to $new_repeats.

repeat_start_position($new_repeat_start_position)

 Title   : repeat_start_position($new_repeat_start_position)
 Usage   : my $repeat_start_position =
        $o_usat->repeat_start_position($new_repeat_start_position) _or_
        my $repeat_start_position = $o_usat->repeat_start_position()
 Function: Get/Set the repeat repeat_start_position for this
        Microsatellite
 Returns : A scalar representing the repeat start position for this 
        Microsatellite.
 Args    : If provided, the current repeat start position of this
        Microsatellite will be set to $new_repeat_start_position.
        This method will also try to set the repeat end position. This
        depends on having information for the motif and the number of
        repeats. If you want to use methods like get_trailing_flank or
        get_leading flank, be careful to include the right information.

repeat_end_position($value)

 Title   : repeat_end_position($set)
 Usage   : $new_repeat_end_position =
                $o_usat->repeat_end_position("set"); _or_
        $new_repeat_end_position =
                $o_usat->repeat_end_position($value); _or_
        $current_repeat_end_position = $o_usat->repeat_end_position();
 Function: get/set the end position of the repeat in this sequence
 Returns : A scalar representing the base index of the end of the
        repeat in this Microsatellite. The first base in the sequence
        is base 1.
 Args    : A scalar representing a value, the string "set", or no
        argument (see Notes).
 Notes   : If you do not provide an argument to this method, the current
        end position of the repeat in this Microsatellite will be
        returned (a scalar).
        If you provide the string "set" to this method it will set the
        end position based on the start position, the length of the
        motif, and the nuimber of repeats.
        If you specify a value the current end position of the repeat
        will be set to that value. This is a really bad idea. Don't do
        it.

equals

 Title   : equals
 Usage   : if( $mappable->equals($mapable2)) ...
 Function: Test if a position is equal to another position
 Returns : boolean
 Args    : Bio::Map::MappableI

less_than

 Title   : less_than
 Usage   : if( $mappable->less_than($m2) ) ...
 Function: Tests if a position is less than another position
 Returns : boolean
 Args    : Bio::Map::MappableI

greater_than

 Title   : greater_than
 Usage   : if( $mappable->greater_than($m2) ) ...
 Function: Tests if position is greater than another position
 Returns : boolean
 Args    : Bio::Map::MappableI

get_leading_flank()

 Title   : get_leading_flank()
 Usage   : $leading_sequence = $o_usat->get_leading_flank();
 Returns : A scalar representing the sequence before the repeats in this
        Microsatellite.
 Args    : None.

get_trailing_flank()

 Title   : get_trailing_flank()
 Usage   : $trailing_flank = $o_usat->get_trailing_flank();
 Returns : A scalar representing the sequence after the repeats in this
        Microsatellite.
 Args    : None.