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HMMER User's Guide HMMER User's Guide Biological sequence analysis using pro®le hidden Markov models http://hmmer.wustl.edu/ Version 2.1.1; December 1998 Sean Eddy Dept. of Genetics, Washington University School of Medicine 4566 Scott Ave., St. Louis, MO 63110, USA [email protected] With contributions by Ewan Birney ([email protected]) Copyright (C) 1992-1998, 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 modi®ed 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 ®les 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 5 1.1 The programs in HMMER . 5 1.2 Files used in the tutorial . 6 1.3 Searching a sequence database with a single pro®le HMM . 6 HMM construction with hmmbuild . 7 HMM calibration with hmmcalibrate . 7 Sequence database search with hmmsearch . 8 Searching major databases like NR or SWISSPROT . 11 Local alignment searches with hmmsearch . 11 1.4 Searching a query sequence against a pro®le HMM database . 12 Creating your own pro®le HMM database . 12 Parsing the domain structure of a sequence with hmmpfam . 12 Downloading the PFAM database . 13 1.5 Maintaining multiple alignments with hmmalign . 14 2 Introduction 15 2.1 Pro®le HMMs . 15 2.2 Primary changes from HMMER 1.x . 16 2.3 Plan 7 . 17 The Plan 7 architecture . 17 Local alignments in Plan 7 . 18 The Plan 7 null model . 19 Wing retraction in Plan 7 dynamic programming . 20 2.4 Sequence ®le formats . 20 2.5 Command line options . 21 2.6 Environment variables . 21 2.7 Other pro®le HMM implementations . 22 3 Manual pages 23 3.1 HMMER - pro®le hidden Markov model software . 23 Synopsis . 23 Description . 23 Options . 24 Sequence File Formats . 24 Environment Variables . 24 3.2 hmmalign - align sequences to an HMM pro®le . 25 Synopsis . 25 2 Description . 25 Options . 25 Expert Options . 25 3.3 hmmbuild - build a pro®le HMM from an alignment . 26 Synopsis . 26 Description . 26 Options . 26 Expert Options . 27 3.4 hmmcalibrate - calibrate HMM search statistics . 30 Synopsis . 30 Description . 30 Options . 30 Expert Options . 30 3.5 hmmconvert - convert between pro®le HMM ®le formats . 32 Synopsis . 32 Description . 32 Options . 32 3.6 hmmemit - generate sequences from a pro®le HMM . 33 Synopsis . 33 Description . 33 Options . 33 Expert Options . 33 3.7 hmmfetch - retrieve an HMM from an HMM database . 34 Synopsis . 34 Description . 34 Options . 34 3.8 hmmindex - create a binary GSI index for an HMM database . 35 Synopsis . 35 Description . 35 Options . 35 3.9 hmmpfam - search a single sequence against an HMM database . 36 Synopsis . 36 Description . 36 Options . 36 Expert Options . 37 3.10 hmmsearch - search a sequence database with a pro®le HMM . 39 Synopsis . 39 Description . 39 Options . 39 Expert Options . 40 3.11 alistat - show statistics for a multiple alignment ®le . 41 Synopsis . 41 Description . 41 Options . 41 3.12 getseq - get a sequence from a ¯at®le database. 42 Synopsis . 42 Description . 42 3 Options . 42 3.13 seqstat - show statistics and format for a sequence ®le . 44 Synopsis . 44 Description . 44 Options . ..
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