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NAME

Bio::SeqAlignment::Components::Sundry::Tailing - Add various tails to sequences

VERSION

version 0.01

SYNOPSIS

  use Bio::SeqAlignment::Components::Sundry::Tailing;
  my $modifications_HoH = add_polyA( $bioseq_objects, $taildist, $seed, @distparams );

DESCRIPTION

This module provides functions to add various tails to the 3' of biological sequences. Such modifications are useful for e.g. simulating polyA tails in RNAseq, adding UMI tags to sequences, etc.

EXPORT

add_polyA

SUBROUTINES

add_polyA

  my $modifications_HoH = add_polyA( $bioseq_objects, $taildist, $seed, @distparams );

Add a polyA tail to each sequence in the array of biological sequence objects. The functiontakes a reference to an array of biological sequence objects (e.g. Bio::Seq,BioX::Seq, FAST::Bio::Seq, or anything that provides a seq and id method), a possibly truncated tail distribution from the Gnu Scientific Library, a seed and a list of distribution parameters for the tail distribution. The function modifies the array in situ and returns a reference to a hash of modifications (i.e. the position the polyA tail was added as well as its length. Note that this function uses simulation to generate a tail of random length.

SEE ALSO

  • Bio::SeqAlignment::Examples::TailingPolyester

    A collection of examples that demonstrate how to extend the polyester RNA sequencing tool by including polyA tails in the reference RNA being used to generate the simulated RNA sequencing data.

AUTHOR

Christos Argyropoulos <chrisarg *at* cpan.org>

COPYRIGHT AND LICENSE

This software is copyright (c) 2024 by Christos Argyropoulos.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.