/ 
Alien-SeqAlignment-last-0.02
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/ Alien::SeqAlignment::last

NAME

Alien::SeqAlignment::edlib - find, build and install the last tools

VERSION

version 0.02

SYNOPSIS

To execute the last set of tools, you can use the following code:

use Alien::SeqAlignment::last;
use Env qw( @PATH );
unshift @PATH, Alien::SeqAlignment::last->bin_dir;

Now you can run the last tools as:

system Alien::SeqAlignment::last->lastal (options);    
system Alien::SeqAlignment::last->lastdb (options); 
system Alien::SeqAlignment::last->maf_convert (options); 
system Alien::SeqAlignment::last->train (options); 
system Alien::SeqAlignment::last->split_or_splice (options); 
system Alien::SeqAlignment::last->split_or_splice_pe (options); 
system Alien::SeqAlignment::last->pe_probs (options);

DESCRIPTION

This distribution provides last so that it can be used by other Perl distributions that are on CPAN. The source code will be downloaded from the last Gitlab repo, and if that fails it will use the location of a fork by the author of this Perl module. The build provides the various CLI tools in the last and last-pair-pe suites. Parallelization requires the installation of the GNU parallel package. If this is not available, the installation will terminate. In that case, install GNU Parallel from https://www.gnu.org/software/parallel/ and re-attempt installation of this Alien.

METHODS

lastal

Alien::SeqAlignment::last->lastal

Returns the command name for running the CLI version of the last aligner. The latter finds local alignments between query sequences, and reference sequences that have been collected into a database using lastdb.

dbbuild

Alien::SeqAlignment::last->dbbuild

Returns the command name for the application that builds the database of the reference sequences.

maf_convert

Alien::SeqAlignment::last->maf_convert

Interconverts the MAF format with other multiple alignment formats. The formats currently supported are: axt, bed, blast, blasttab, chain, gff, html, psl, sam, tab. Note that per the author of last, the blast format is merely "blast-like", i.e. not identical to NCBI BLAST.

last_train

Alien::SeqAlignment::last->last_train

last-train finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences. It thereby finds suitable substitution and gap scores for aligning them.

split_or_splice

Alien::SeqAlignment::last->split_or_splice

This commnd provides access to last-split, which finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA).

split_or_splice_for_pe

Alien::SeqAlignment::last->split_or_splice_for_pe

This commnd provides access to last-split, which finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA). It specifically targets paired-end reads. last-split-pe is a method that can split-align a short DNA read to a reference genome. It achieves high accuracy by combining probabilistic alignments with information from paired-end reads.

pe_probs

Alien::SeqAlignment::last->pe_probs

This commnd provides access to last-pair-probs, which reads candidate alignments of paired DNA reads to a genome, and:

* estimates the distribution of distances between paired reads, * estimates the probability that each alignment represents the genomic source of the read. These probabilities corresponds to a split alignment of the pair end read.

SEE ALSO

  • LAST

    LAST: find & align related regions of sequences LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes). It's especially good at:

    * Finding rearrangements and recombinations: the primary author claims that last-split does that more rigorously than anything else. * Finding DNA-versus-protein related regions, especially protein fossils. * Unusual data, e.g. AT-rich DNA, because we can fit parameters to the data and calculate significance. * Sensitive DNA-DNA search, due to fitting, sensitive seeding, and calculating significance.

    It can also: indicate the confidence/uncertainty of each column in an alignment, and use sequence quality data in a rigorous fashion.

  • last-split-pe

    last-split-pe is a method that can split-align a short DNA read to a reference genome. It achieves high accuracy by combining probabilistic alignments with information from paired-end reads.

  • Alien

    Documentation on the Alien concept itself.

  • Alien::Base

    The base class for this Alien. The methods in that class allow you to use the static and the dynamic edlib library in your code.

  • Alien::Build::Manual::AlienUser

    Detailed manual for users of Alien classes.

  • Bio::SeqAlignment

    A collection of tools and libraries for aligning biological sequences from within Perl.

AUTHOR

Christos Argyropoulos <chrisarg@gmail.com>

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.