NAME

       Stone::GB_Sequence - Specialized Access to GenBank Records

SYNOPSIS

         use Boulder::Genbank;  # No need to use Stone::GB_Sequence directly
         $gb = Boulder::Genbank->newFh qw(M57939 M28274 L36028);

         while ($entry = <$gb>) {
           print "Entry's length is ",$entry->length,"\n";
           @cds   = $entry->match_features(-type=>'CDS');
           @exons = $entry->match_features(-type=>'Exon',-start=>100,-end=>300);
         }
       }

DESCRIPTION

       Stone::GB_Sequence provides several specialized access methods to the various fields in a
       GenBank flat file record.  You can return the sequence as a Bio::Seq object, or query the
       sequence for features that match positional or descriptional criteria that you provide.

CONSTRUCTORS

       This class is not intended to be created directly, but via a Boulder::Genbank stream.

METHODS

       In addition to the standard Stone methods and accessors, the following methods are
       provided.  In the synopses, the variable $entry refers to a previously-created
       Stone::GB_Sequence object.

   $length = $entry->length
       Get the length of the sequence.

   $start = $entry->start
       Get the start position of the sequence, currently always "1".

   $end = $entry->end
       Get the end position of the sequence, currently always the same as the length.

   @feature_list = $entry->features(-pos=>[50,450],-type=>['CDS','Exon'])
       features() will search the entry feature list for those features that meet certain
       criteria.  The criteria are specified using the -pos and/or -type argument names, as shown
       below.

       -pos
           Provide a position or range of positions which the feature must overlap.  A single
           position is specified in this way:

              -pos => 1500;         # feature must overlap postion 1500

           or a range of positions in this way:

              -pos => [1000,1500];  # 1000 to 1500 inclusive

           If no criteria are provided, then features() returns all the features, and is
           equivalent to calling the Features() accessor.

       -type, -types
           Filter the list of features by type or a set of types.  Matches are case-insensitive,
           so "exon", "Exon" and "EXON" are all equivalent.  You may call with a single type as
           in:

              -type => 'Exon'

           or with a list of types, as in

              -types => ['Exon','CDS']

           The names "-type" and "-types" can be used interchangeably.

   $seqObj = $entry->bioSeq;
       Returns a Bio::Seq object from the Bioperl project.  Dies with an error message unless the
       Bio::Seq module is installed.

AUTHOR

       Lincoln D. Stein <lstein@cshl.org>.

COPYRIGHT

       Copyright 1997-1999, Cold Spring Harbor Laboratory, Cold Spring Harbor NY.  This module
       can be used and distributed on the same terms as Perl itself.

SEE ALSO

       Boulder, <Boulder:Genbank>, Stone