HMMER on Helix
Profile hidden Markov models for biological sequence analysis
Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER uses profile HMMs, and can be useful in situations like:- if you are working with an evolutionarily diverse protein family, a BLAST search with any individual sequence may not find the rest of the sequences in the family.
- the top hits in a BLAST search are hypothetical sequences from genome projects.
- your protein consists of several domains which are of different types.
HMMER (pronounced 'hammer', as in a more precise mining tool than BLAST) was developed by Sean Eddy at Washington University in St. Louis. The HMMER website is hmmer.janelia.org.
HMMER User Guide
(PDF)
HMMER programs
| hmmalign | align sequences to an HMM profile |
| hmmbuild | build a hidden Markov model from an alignment |
| hmmcalibrate | calibrate HMM search statistics |
| hmmconvert | convert between profile HMM file formats |
| hmmedit | generate sequences from a profile HMM |
| hmmfetch | retrieve specific HMM from an HMM database |
| hmmindex | create SSI index for an HMM database |
| hmmpfam | search one or more sequences against HMM database |
| hmmsearch | search a sequence database with a profile HMM |
Version
The output of the HMMER programs include the version number at the top.
Running a HMMER program on Helix
HMMER programs can be run interactively on Helix.Sample run (user input in bold):
[user@helix mydir]$ hmmpfam /fdb/fastadb/pfam/Pfam_ls myseq hmmpfam - search one or more sequences against HMM database HMMER 2.3.2 (Oct 2003) Copyright (C) 1992-2003 HHMI/Washington University School of Medicine Freely distributed under the GNU General Public License (GPL) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /fdb/fastadb/pfam/Pfam_ls Sequence file: myseq - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query sequence: 7LES_DROME Accession: P13368 Description: SEVENLESS PROTEIN (EC 2.7.1.112). Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- --------- --- Pkinase_Tyr Protein tyrosine kinase 487.3 1.8e-143 1 fn3 Fibronectin type III domain 177.0 4.9e-50 6 Pkinase Protein kinase domain 134.0 4.3e-37 1 Ldl_recept_b Low-density lipoprotein receptor repe 9.0 0.18 1 Vicilin_N Vicilin N terminal region -89.9 1.7 1 DUF1478 Protein of unknown function (DUF1478) -86.2 1.8 1 Cys_knot Cystine-knot domain -39.0 2 1 NHL NHL repeat 7.7 2 1 LSR Lipolysis stimulated receptor (LSR) -19.2 2 1 APH Phosphotransferase enzyme family -35.1 2.1 1 Fzo_mitofusin fzo-like conserved region -100.4 3.2 1 [...]
