LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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http://www.apache.org/licenses/LICENSE-2.0

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NAME

Bio::EnsEMBL::Utils::Sequence - Utility functions for sequences

SYNOPSIS

use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp expand);

my $seq = 'ACTTTAAAGGCTATCCCAATATG';

print "my sequence = $seq\n";

reverse_comp( \$seq );

print "my reverse comp = $seq\n";

my $compressed_seq = '(AC)3';

print "my expanded seq is = expand($compressed_seq)";

METHODS

reverse_comp

Arg [1]    : reference to a string $seqref
Example    : use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);

             $seq = 'ACCTGAA';
             reverse_comp(\$seq);
             print $seq;

Description: Does an in place reverse compliment of a passed in string
             reference.  The string is passed by reference
             rather than by value for memory efficiency.
Returntype : none
Exceptions : none
Caller     : SequenceAdaptor, SliceAdaptor

expand

Arg [1]    : reference to a string $seqref
Example    : use Bio::EnsEMBL::Utils::Sequence qw(expand);

             $seq = '(AC)3';
             expand(\$seq);
             print $seq;
            

Description: Expands a genomic sequence. The string is passed by reference
             rather than by value for memory efficiency.
Returntype : none
Exceptions : none
Caller     : SequenceAdaptor, SliceAdaptor