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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NAME

Bio::EnsEMBL::Utils::PolyA

SYNOPSIS

my $seq;    # a Bio::Seq object
my $polyA = Bio::EnsEMBL::Utils::PolyA->new();

# returns a new Bio::Seq object with the trimmed sequence
my $trimmed_seq = $polyA->clip($seq);

# cat put Ns in the place of the polyA/polyT tail
my $masked_seq = $polyA->mask($seq);

# can put in lower case the polyA/polyT using any flag:
my $softmasked_seq = $poly->mask( $seq, 'soft' );

DESCRIPTION

It reads a Bio::Seq object, it first finds out whether it has a
polyA or a polyT and then performs one operation in the seq string:
clipping, masking or softmasking.  It then returns a new Bio::Seq
object with the new sequence.

METHODS

new