.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10. .TH HHBLITS "1" "June 2012" "hhblits 2.0.15" "User Commands" .SH NAME hhblits \- fast homology detection method to iteratively search a HMM database .SH SYNOPSIS .B hhblits \fI\-i query \fR[\fIoptions\fR] .SH DESCRIPTION HHblits version 2.0.15 (June 2012): HMM\-HMM\-based lightning\-fast iterative sequence search HHblits is a sensitive, general\-purpose, iterative sequence search tool that represents both query and database sequences by HMMs. You can search HHblits databases starting with a single query sequence, a multiple sequence alignment (MSA), or an HMM. HHblits prints out a ranked list of database HMMs/MSAs and can also generate an MSA by merging the significant database HMMs/MSAs onto the query MSA. .PP Remmert M., Biegert A., Hauser A., and Soding J. HHblits: Lightning\-fast iterative protein sequence searching by HMM\-HMM alignment. Nat. Methods 9:173\-175 (2011) (C) Johannes Soeding, Michael Remmert, Andreas Biegert, Andreas Hauser .TP \fB\-i\fR input/query: single sequence or multiple sequence alignment (MSA) in a3m, a2m, or FASTA format, or HMM in hhm format .PP may be 'stdin' or 'stdout' throughout. .SH OPTIONS .TP \fB\-d\fR database name (e.g. uniprot20_29Feb2012) (default=) .TP \fB\-n\fR [1,8] number of iterations (default=2) .TP \fB\-e\fR [0,1] E\-value cutoff for inclusion in result alignment (def=0.001) .SS "Input alignment format:" .TP \fB\-M\fR a2m use A2M/A3M (default): upper case = Match; lower case = Insert; .IP \&' \-' = Delete; '.' = gaps aligned to inserts (may be omitted) .TP \fB\-M\fR first use FASTA: columns with residue in 1st sequence are match states .TP \fB\-M\fR [0,100] use FASTA: columns with fewer than X% gaps are match states .SS "Output options:" .TP \fB\-o\fR write results in standard format to file (default=) .TP \fB\-oa3m\fR write result MSA with significant matches in a3m format .TP \fB\-opsi\fR write result MSA of significant matches in PSI\-BLAST format .TP \fB\-oa2m\fR write result MSA of significant matches in a2m format .TP \fB\-ohhm\fR write HHM file for result MSA of significant matches .TP \fB\-oalis\fR write MSAs in A3M format after each iteration .TP \fB\-Ofas\fR write pairwise alignments of significant matches in FASTA format Analogous for output in a3m, a2m, and psi format (e.g. \fB\-Oa3m\fR) .TP \fB\-qhhm\fR write query input HHM file of last iteration (default=off) .TP \fB\-seq\fR max. number of query/template sequences displayed (default=1) .TP \fB\-aliw\fR number of columns per line in alignment list (default=80) .TP \fB\-p\fR [0,100] minimum probability in summary and alignment list (default=20) .TP \fB\-E\fR [0,inf[ maximum E\-value in summary and alignment list (default=1E+06) .TP \fB\-Z\fR maximum number of lines in summary hit list (default=500) .TP \fB\-z\fR minimum number of lines in summary hit list (default=10) .TP \fB\-B\fR maximum number of alignments in alignment list (default=500) .TP \fB\-b\fR minimum number of alignments in alignment list (default=10) .PP Prefilter options .TP \fB\-noprefilt\fR disable all filter steps .TP \fB\-noaddfilter\fR disable all filter steps (except for fast prefiltering) .TP \fB\-nodbfilter\fR disable additional filtering of prefiltered HMMs .HP \fB\-noblockfilter\fR search complete matrix in Viterbi .TP \fB\-maxfilt\fR max number of hits allowed to pass 2nd prefilter (default=20000) .PP Filter options applied to query MSA, database MSAs, and result MSA .TP \fB\-all\fR show all sequences in result MSA; do not filter result MSA .TP \fB\-id\fR [0,100] maximum pairwise sequence identity (def=90) .TP \fB\-diff\fR [0,inf[ filter MSAs by selecting most diverse set of sequences, keeping at least this many seqs in each MSA block of length 50 (def=1000) .TP \fB\-cov\fR [0,100] minimum coverage with master sequence (%) (def=0) .TP \fB\-qid\fR [0,100] minimum sequence identity with master sequence (%) (def=0) .TP \fB\-qsc\fR [0,100] minimum score per column with master sequence (default=\-20.0) .TP \fB\-neff\fR [1,inf] target diversity of multiple sequence alignment (default=off) .SS "HMM\-HMM alignment options:" .TP \fB\-norealign\fR do NOT realign displayed hits with MAC algorithm (def=realign) .TP \fB\-mact\fR [0,1[ posterior probability threshold for MAC re\-alignment (def=0.350) Parameter controls alignment greediness: 0:global >0.1:local .TP \fB\-glob\fR/\-loc use global/local alignment mode for searching/ranking (def=local) .TP \fB\-realign_max\fR realign max. hits (default=1000) .TP \fB\-alt\fR show up to this many significant alternative alignments(def=2) .HP \fB\-premerge\fR merge hits to query MSA before aligning remaining hits (def=3) .TP \fB\-shift\fR [\-1,1] profile\-profile score offset (def=\-0.03) .TP \fB\-ssm\fR {0,..,4} 0: no ss scoring 1,2: ss scoring after or during alignment [default=2] 3,4: ss scoring after or during alignment, predicted vs. predicted .TP \fB\-ssw\fR [0,1] weight of ss score (def=0.11) .SS "Gap cost options:" .TP \fB\-gapb\fR [0,inf[ Transition pseudocount admixture (def=1.00) .TP \fB\-gapd\fR [0,inf[ Transition pseudocount admixture for open gap (default=0.15) .TP \fB\-gape\fR [0,1.5] Transition pseudocount admixture for extend gap (def=1.00) .TP \fB\-gapf\fR ]0,inf] factor to increase/reduce gap open penalty for deletes (def=0.60) .TP \fB\-gapg\fR ]0,inf] factor to increase/reduce gap open penalty for inserts (def=0.60) .TP \fB\-gaph\fR ]0,inf] factor to increase/reduce gap extend penalty for deletes(def=0.60) .TP \fB\-gapi\fR ]0,inf] factor to increase/reduce gap extend penalty for inserts(def=0.60) .TP \fB\-egq\fR [0,inf[ penalty (bits) for end gaps aligned to query residues (def=0.00) .TP \fB\-egt\fR [0,inf[ penalty (bits) for end gaps aligned to template residues (def=0.00) .SS "Pseudocount (pc) options:" .TP \fB\-pcm\fR {0,..,2} position dependence of pc admixture 'tau' (pc mode, default=2) 0: no pseudo counts: tau = 0 1: constant tau = a 2: diversity\-dependent: tau = a/(1 + ((Neff[i]\-1)/b)^c) (Neff[i]: number of effective seqs in local MSA around column i) .TP \fB\-pca\fR [0,1] overall pseudocount admixture (def=1.0) .TP \fB\-pcb\fR [1,inf[ Neff threshold value for \fB\-pcm\fR 2 (def=1.5) .TP \fB\-pcc\fR [0,3] extinction exponent c for \fB\-pcm\fR 2 (def=1.0) .TP \fB\-pre_pca\fR [0,1] PREFILTER pseudocount admixture (def=0.8) .HP \fB\-pre_pcb\fR [1,inf[ PREFILTER threshold for Neff (def=1.8) .SS "Context\-specific pseudo\-counts:" .TP \fB\-nocontxt\fR use substitution\-matrix instead of context\-specific pseudocounts .HP \fB\-contxt\fR context file for computing context\-specific pseudocounts (default=/usr/lib/hhsuite/data/context_data.lib) .TP \fB\-cslib\fR column state file for fast database prefiltering (default=/usr/lib/hhsuite/data/cs219.lib) .PP Predict secondary structure .TP \fB\-addss\fR add 2ndary structure predicted with PSIPRED to result MSA .HP \fB\-psipred\fR directory with PSIPRED executables (default=) .TP \fB\-psipred_data\fR directory with PSIPRED data (default=) .SS "Other options:" .TP \fB\-v\fR verbose mode: 0:no screen output 1:only warings 2: verbose (def=2) .HP \fB\-neffmax\fR ]1,20] skip further search iterations when diversity Neff of query MSA .IP becomes larger than neffmax (default=10.0) .TP \fB\-cpu\fR number of CPUs to use (for shared memory SMPs) (default=2) .HP \fB\-scores\fR write scores for all pairwise comparisions to file .TP \fB\-atab\fR write all alignments in tabular layout to file .TP \fB\-maxres\fR max number of HMM columns (def=15002) .HP \fB\-maxmem\fR [1,inf[ max available memory in GB (def=3.0) .SH EXAMPLES hhblits \fB\-i\fR query.fas \fB\-o\fR query.hhr \fB\-d\fR .PP hhblits \fB\-i\fR query.fas \fB\-o\fR query.hhr \fB\-oa3m\fR query.a3m \fB\-n\fR 1 \fB\-d\fR .PP Download databases from ftp://toolkit.genzentrum.lmu.de/HH\-suite/databases/ .