HMMER User’s Guide Biological sequence analysis using profile hidden Markov models http://hmmer.wustl.edu/ Version 2.2; August 2001 Sean Eddy Howard Hughes Medical Institute and Dept. of Genetics Washington University School of Medicine 660 South Euclid Avenue, Box 8232 Saint Louis, Missouri 63110, USA [email protected] With contributions by Ewan Birney ([email protected]) Copyright (C) 1992-2001, Washington University in St. Louis. 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. The HMMER software package is a copyrighted work that may be freely distributed and modified under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. Some versions of HMMER may have been obtained under specialized commercial licenses from Washington University; for details, see the files COPYING and LICENSE that came with your copy of the HMMER software. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Appendix for a copy of the full text of the GNU General Public License. 1 Contents 1 Tutorial 6 1.1 The programs in HMMER . 6 1.2 Files used in the tutorial . 7 1.3 Searching a sequence database with a single profile HMM . 7 HMM construction with hmmbuild ............................. 7 HMM calibration with hmmcalibrate ........................... 8 Sequence database search with hmmsearch ......................... 9 Searching major databases like NR or SWISSPROT . 12 Local alignment searches with hmmsearch ......................... 12 1.4 Searching a query sequence against a profile HMM database . 13 Creating your own profile HMM database . 13 Parsing the domain structure of a sequence with hmmpfam . 13 Downloading the PFAM database . 15 1.5 Maintaining multiple alignments with hmmalign ...................... 15 2 Overview 16 2.1 Profile HMMs . 16 2.2 Primary changes from HMMER 1.x . 17 2.3 Plan 7 . 18 The Plan 7 architecture . 18 Local alignments in Plan 7 . 19 The Plan 7 null model . 20 Wing retraction in Plan 7 dynamic programming . 21 2.4 Sequence file formats . 21 2.5 Command line options . 22 2.6 Environment variables . 22 2.7 Other profile HMM implementations . 23 3 Stray topics 24 3.1 Evaluating the significance of profile HMM hit . 24 Executive summary . 24 In more detail: What HMMER raw scores mean . 25 In more detail: What HMMER E-values mean . 26 In more detail: What Pfam TC/NC/GA cutoffs mean . 27 3.2 How do I cite HMMER? . 28 2 4 Manual pages 29 4.1 HMMER - profile hidden Markov model software . 29 Synopsis . 29 Description . 29 Options . 29 Sequence File Formats . 30 Environment Variables . 30 4.2 hmmalign - align sequences to an HMM profile . 31 Synopsis . 31 Description . 31 Options . 31 Expert Options . 31 4.3 hmmbuild - build a profile HMM from an alignment . 33 Synopsis . 33 Description . 33 Options . 33 Expert Options . 34 4.4 hmmcalibrate - calibrate HMM search statistics . 37 Synopsis . 37 Description . 37 Options . 37 Expert Options . 37 4.5 hmmconvert - convert between profile HMM file formats . 39 Synopsis . 39 Description . 39 Options . 39 4.6 hmmemit - generate sequences from a profile HMM . 40 Synopsis . 40 Description . 40 Options . 40 Expert Options . 40 4.7 hmmfetch - retrieve an HMM from an HMM database . 41 Synopsis . 41 Description . 41 Options . 41 4.8 hmmindex - create a binary SSI index for an HMM database . 42 Synopsis . 42 Description . 42 Options . 42 4.9 hmmpfam - search one or more sequences against an HMM database . 43 Synopsis . 43 Description . 43 Options . 43 Expert Options . 44 4.10 hmmsearch - search a sequence database with a profile HMM . 46 Synopsis . 46 Description . 46 3 Options . 46 Expert Options . 47 4.11 afetch - retrieve an alignment from an alignment database . 49 Synopsis . 49 Description . 49 Options . 49 Expert Options . 49 4.12 alistat - show statistics for a multiple alignment file . 50 Synopsis . 50 Description . 50 Options . 50 Expert Options . ..