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HMMER User's Guide HMMER User’s Guide Biological sequence analysis using profile hidden Markov models http://hmmer.org/ Version 3.0rc1; February 2010 Sean R. Eddy for the HMMER Development Team Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 USA http://eddylab.org/ Copyright (C) 2010 Howard Hughes Medical Institute. Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are retained on all copies. HMMER is licensed and freely distributed under the GNU General Public License version 3 (GPLv3). For a copy of the License, see http://www.gnu.org/licenses/. HMMER is a trademark of the Howard Hughes Medical Institute. 1 Contents 1 Introduction 5 How to avoid reading this manual . 5 How to avoid using this software (links to similar software) . 5 What profile HMMs are . 5 Applications of profile HMMs . 6 Design goals of HMMER3 . 7 What’s still missing in HMMER3 . 8 How to learn more about profile HMMs . 9 2 Installation 10 Quick installation instructions . 10 System requirements . 10 Multithreaded parallelization for multicores is the default . 11 MPI parallelization for clusters is optional . 11 Using build directories . 12 Makefile targets . 12 3 Tutorial 13 The programs in HMMER . 13 Files used in the tutorial . 13 Searching a sequence database with a single profile HMM . 14 Step 1: build a profile HMM with hmmbuild . 14 Step 2: search the sequence database with hmmsearch . 16 Searching a profile HMM database with a query sequence . 22 Step 1: create an HMM database flatfile . 22 Step 2: compress and index the flatfile with hmmpress . 22 Step 3: search the HMM database with hmmscan . 23 Creating multiple alignments with hmmalign . 24 Single sequence queries using phmmer . 25 Iterative searches using jackhmmer . 25 4 Manual pages 28 hmmalign - align sequences to a profile HMM . 28 Synopsis . 28 Description . 28 Options . 28 hmmbuild - construct profile HMM(s) from multiple sequence alignment(s) . 30 Synopsis . 30 Description . 30 Options . 30 Options for specifying the alphabet . 30 Options controlling profile construction . 30 Options controlling relative weights . 31 Options controlling effective sequence number . 31 Options controlling e-value calibration . 32 Other options . 33 hmmconvert - convert profile file to a HMMER format . 34 Synopsis . 34 Description . 34 Options . 34 2 hmmemit - sample sequences from a profile HMM . 35 Synopsis . 35 Description . 35 Common options . 35 Options controlling emission from profiles . 35 Other options . 36 hmmfetch - retrieve profile HMM(s) from a file . 37 Synopsis . 37 Description . 37 Options . 37 hmmpress - prepare an HMM database for hmmscan . 38 Synopsis . 38 Description . 38 Options . 38 hmmscan - search sequence(s) against a profile database . 39 Synopsis . 39 Description . 39 Options . 39 Options for controlling output . 39 Options for reporting thresholds . 40 Options for inclusion thresholds . 40 Options for model-specific score thresholding . 41 Control of the acceleration pipeline . 41 Other options . 42 hmmsearch - search profile(s) against a sequence database . 43 Synopsis . 43 Description . 43 Options . 43 Options for controlling output . 43 Options controlling reporting thresholds . 44 Options for inclusion thresholds . 44 Options for model-specific score thresholding . 45 Options controlling the acceleration pipeline . 45 Other options . 46 hmmsim - collect score distributions on random sequences . 47 Synopsis . 47 Description . 47 Miscellaneous options . 48 Options controlling output . 48 Options controlling model configuration (”mode”) . 49 Options controlling scoring algorithm . ..
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