NAME

Alien::SeqAlignment::hmmer3 - find, build and install the hmmer3 tools

VERSION

version 0.03

SYNOPSIS

To execute the hmmer3 set of tools, you can use the following code:

use Alien::SeqAlignment::hmmer3;
use Env qw( @PATH );
unshift @PATH, Alien::SeqAlignment::hmmer3->bin_dir;

Now you can run the hmmer3 tools as:

HMMER3 SUITE

system Alien::SeqAlignment::hmmer3->alimask       (parameters & options);
system Alien::SeqAlignment::hmmer3->hmmalign      (parameters & options);
system Alien::SeqAlignment::hmmer3->hmmbuild      (parameters & options);
system Alien::SeqAlignment::hmmer3->hmmconvert    (parameters & options);
system Alien::SeqAlignment::hmmer3->hmmemit       (parameters & options);
system Alien::SeqAlignment::hmmer3->hmmfetch      (parameters & options);
system Alien::SeqAlignment::hmmer3->hmmlogo       (parameters & options);
system Alien::SeqAlignment::hmmer3->hmmpgmd       (parameters & options);
system Alien::SeqAlignment::hmmer3->hmmpgmd_shard (parameters & options);
system Alien::SeqAlignment::hmmer3->hmmpress      (parameters & options);
system Alien::SeqAlignment::hmmer3->hmmsearch     (parameters & options);
system Alien::SeqAlignment::hmmer3->hmmsim        (parameters & options);
system Alien::SeqAlignment::hmmer3->hmmstat       (parameters & options);
system Alien::SeqAlignment::hmmer3->jackhmmer     (parameters & options);
system Alien::SeqAlignment::hmmer3->makehmmerdb   (parameters & options);
system Alien::SeqAlignment::hmmer3->nhmmer        (parameters & options);
system Alien::SeqAlignment::hmmer3->nhmmscan      (parameters & options);
system Alien::SeqAlignment::hmmer3->phmmer        (parameters & options);

EASEL SUITE

system Alien::SeqAlignment::hmmer3->esl_afetch     (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_alimanip   (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_alimap     (parameters & options);
system Alien::SeqAlignment::hmmer3->asl_alimask    (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_alimerge   (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_alipid     (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_alirev     (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_alistat    (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_compalign  (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_compstruct (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_construct  (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_histplot   (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_mask       (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_mixdchlet  (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_reformat   (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_selectn    (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_seqrange   (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_seqstat    (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_sfetch     (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_shuffle    (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_ssdraw     (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_translate  (parameters & options);
system Alien::SeqAlignment::hmmer3->esl_weight     (parameters & options);

DESCRIPTION

This distribution provides HMMER3 so that it can be used by other Perl distributions that are on CPAN. The source code will be downloaded from the HMMER3 website, if the HMMER3 is not found in the system path. The url used is : http://eddylab.org/software/hmmer/hmmer.tar.gz The program will then be built and installed in a private share location. The build provides the various CLI tools in the hmmer3 AND Easel suites. Note that the Easel tools are also provided by the HMMER3 suite and this Alien assumes that Easel has been previously installed with HMMER3 during a prior system install. If this is not the case, attempt to use the Easel files will terminate any Perl programs that try to use the Easel tools from within this distribution.

METHODS : HMMER3 SUITE

alimask

Alien::SeqAlignment::hmmer3->alimask  (parameters & options);

alimask - add column mask to a multiple sequence alignment

hmmalign

Alien::SeqAlignment::hmmer3->hmmalign (parameters & options);

hmmalign - make multiple sequence alignment using a profile

hmmbuild

Alien::SeqAlignment::hmmer3->hmmbuild (parameters & options);

hmmbuild - build profile from input multiple alignment

hmmconvert

Alien::SeqAlignment::hmmer3->hmmconvert (parameters & options);

hmmconvert - convert between different profile file formats

hmmemit

Alien::SeqAlignment::hmmer3->hmmemit (parameters & options);

hmmemit - generate (sample) sequences from a profile

hmmfetch

Alien::SeqAlignment::hmmer3->hmmfetch (parameters & options);

hmmfetch - retrieve profile(s) from a profile file

hmmlogo

Alien::SeqAlignment::hmmer3->hmmlogo (parameters & options);

hmmlogo - produce a conservation logo graphic from a profile

hmmpgmd

Alien::SeqAlignment::hmmer3->hmmpgmd (parameters & options);

hmmpgmd - search daemon for the hmmer.org website

hmmpgmd_shard

Alien::SeqAlignment::hmmer3->hmmpgmd_shard (parameters & options);

hmmpgmd_shard - sharded search daemon for the hmmer.org website

hmmscan

Alien::SeqAlignment::hmmer3->hmmscan (parameters & options);

hmmscan - search sequence(s) against a profile database

hmmsearch

Alien::SeqAlignment::hmmer3->hmmsearch (parameters & options);  

hmmsearch - search profile against sequence database

hmmpress

Alien::SeqAlignment::hmmer3->hmmpress (parameters & options);

hmmpress - prepare profile database for hmmscan

phmmer

Alien::SeqAlignment::hmmer3->phmmer (parameters & options);

phmmer - search single sequence against sequence database

jackhmmer

Alien::SeqAlignment::hmmer3->jackhmmer (parameters & options);

jackhmmer - iteratively search single sequence against database

nhmmer

Alien::SeqAlignment::hmmer3->nhmmer (parameters & options);

nhmmer - search DNA query against DNA sequence database

nhmmscan

Alien::SeqAlignment::hmmer3->nhmmscan (parameters & options);

nhmmscan - search DNA sequence against a DNA profile database

hmmstat

Alien::SeqAlignment::hmmer3->hmmstat (parameters & options);

hmmstat - show summary statistics for a profile file

makehmmerdb

Alien::SeqAlignment::hmmer3->makehmmerdb (parameters & options);

makehmmerdb - prepare an nhmmer binary database

hmmsim

Alien::SeqAlignment::hmmer3->hmmsim (parameters & options);

hmmsim - collect score distributions on random sequences

METHODS : EASEL SUITE

Note that the names of the methods are the same as the functions in the CLI of the EASEL suite, but with the "-" replaced by "_", e.g. esl-afetch becomes esl_afetch.

esl_afetch

Alien::SeqAlignment::hmmer3->esl_afetch (parameters & options);

esl_afetch - retrieve alignments from a multi-MSA database

esl_alimanip

Alien::SeqAlignment::hmmer3->esl_alimanip (parameters & options);

esl_alimanip - manipulate a multiple sequence alignment

esl_alimap

Alien::SeqAlignment::hmmer3->esl_alimap (parameters & options);

esl_alimap - map two alignments to each other

esl_alimask

Alien::SeqAlignment::hmmer3->esl_alimask (parameters & options);

esl_alimerge

Alien::SeqAlignment::hmmer3->esl_alimerge (parameters & options);

esl_alimerge - merge alignments based on their reference (RF) annotation

esl_alipid

Alien::SeqAlignment::hmmer3->esl_alipid (parameters & options);

esl_alipid - calculate pairwise percent identities for all sequence

esl_alirev

Alien::SeqAlignment::hmmer3->esl_alirev (parameters & options);

esl_alirev - reverse complement a multiple alignment

esl_alistat

Alien::SeqAlignment::hmmer3->esl_alistat (parameters & options);

esl_alistat - summarize a multiple sequence alignment file

esl_compalign

Alien::SeqAlignment::hmmer3->esl_compalign (parameters & options);

esl_compalign - compare two multiple sequence alignments

esl_compstruct

Alien::SeqAlignment::hmmer3->esl_compstruct (parameters & options);

esl_compstruct - calculate accuracy of RNA secondary structure predictions

esl_construct

Alien::SeqAlignment::hmmer3->esl_construct (parameters & options);

esl_construct - describe or create a consensus secondary structure

esl_histplot

Alien::SeqAlignment::hmmer3->esl_histplot (parameters & options);

esl_histplot - collate data histogram, output xmgrace datafile

esl_mask

Alien::SeqAlignment::hmmer3->esl_mask (parameters & options);

esl_mask - mask sequence residues with Xs (or other characters)

esl_mixdchlet

Alien::SeqAlignment::hmmer3->esl_mixdchlet (parameters & options);

esl_mixdchlet - fitting mixture Dirichlets to count data

esl_reformat

Alien::SeqAlignment::hmmer3->esl_reformat (parameters & options);

esl_reformat - convert sequence file formats

esl_selectn

Alien::SeqAlignment::hmmer3->esl_selectn (parameters & options);

esl_selectn - select random subset of lines from file

esl_seqrange

Alien::SeqAlignment::hmmer3->esl_seqrange (parameters & options);

esl_seqrange - determine a range of sequences for one of many parallel

esl_seqstat

Alien::SeqAlignment::hmmer3->esl_seqstat (parameters & options);

esl_seqstat - summarize contents of a sequence file

esl_sfetch

Alien::SeqAlignment::hmmer3->esl_sfetch (parameters & options);

esl_sfetch - retrieve (sub-)sequences from a sequence file

esl_shuffle

Alien::SeqAlignment::hmmer3->esl_shuffle (parameters & options);

esl_shuffle - shuffling sequences or generating random ones

esl_ssdraw

Alien::SeqAlignment::hmmer3->esl_ssdraw (parameters & options);

esl_ssdraw - create postscript secondary structure diagrams

esl_translate

Alien::SeqAlignment::hmmer3->esl_translate (parameters & options);

esl_translate - translate DNA sequence in six frames into individual

esl_weight

Alien::SeqAlignment::hmmer3->esl_weight (parameters & options);

esl_weight - calculate sequence weights in MSA(s)

SEE ALSO

• HMMER

  HMMER: biosequence analysis using profile hidden Markov models

  HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

  HMMER is often used together with a profile database, such as Pfam or many of the databases that participate in Interpro. But HMMER can also work with query sequences, not just profiles, just like BLAST. For example, you can search a protein query sequence against a database with phmmer, or do an iterative search with jackhmmer.

  HMMER is designed to detect remote homologs as sensitively as possible, relying on the strength of its underlying probability models. In the past, this strength came at significant computational expense, but as of the new HMMER3 project, HMMER is now essentially as fast as BLAST.

  HMMER can be downloaded and installed as a command line tool on your own hardware, and now it is also more widely accessible to the scientific community via new search servers at the European Bioinformatics Institute.

• 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.