https://github.com/chrisarg/alien-seqalignment-hmmer3

Sequence Alignment tool
https://github.com/chrisarg/alien-seqalignment-hmmer3
bioinformatics bioinformatics-analysis bioinformatics-scripts sequence-alignment sequencing
Last synced: 11 months ago
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Sequence Alignment tool
Host: GitHub
URL: https://github.com/chrisarg/alien-seqalignment-hmmer3
Owner: chrisarg
License: other
Created: 2024-03-03T14:19:13.000Z (almost 2 years ago)
Default Branch: main
Last Pushed: 2024-03-24T03:44:07.000Z (almost 2 years ago)
Last Synced: 2025-03-25T11:50:21.039Z (11 months ago)
Topics: bioinformatics, bioinformatics-analysis, bioinformatics-scripts, sequence-alignment, sequencing
Language: Perl
Homepage:
Size: 24.4 KB
Stars: 0
Watchers: 1
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README
- Changelog: Changes
- License: LICENSE
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README

          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 

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.
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