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