hhfilter(1) [debian man page]
HHFILTER(1) User Commands HHFILTER(1) NAME
hhfilter - filter an alignment by maximum sequence identity of match states and minimum coverage SYNOPSIS
hhfilter -i infile -o outfile [options] DESCRIPTION
HHfilter version 2.0.15 (June 2012) Filter an alignment by maximum sequence identity of match states and minimum coverage (C) Johannes Soeding, Michael Remmert, Andreas Biegert, Andreas Hauser 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). -i <file> read input file in A3M/A2M or FASTA format -o <file> write to output file in A3M format -a <file> append to output file in A3M format OPTIONS
-v <int> verbose mode: 0:no screen output 1:only warings 2: verbose -id [0,100] maximum pairwise sequence identity (%) (def=90) -diff [0,inf[ filter MSA by selecting most diverse set of sequences, keeping at least this many seqs in each MSA block of length 50 (def=0) -cov [0,100] minimum coverage with query (%) (def=0) -qid [0,100] minimum sequence identity with query (%) (def=0) -qsc [0,100] minimum score per column with query (def=-20.0) -neff [1,inf] target diversity of alignment (default=off) Input alignment format: -M a2m use A2M/A3M (default): upper case = Match; lower case = Insert; '-' = Delete; '.' = gaps aligned to inserts (may be omitted) -M first use FASTA: columns with residue in 1st sequence are match states -M [0,100] use FASTA: columns with fewer than X% gaps are match states Example: hhfilter -id 50 -i d1mvfd_.a2m -o d1mvfd_.fil.a2m hhfilter 2.0.15 June 2012 HHFILTER(1)
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HHBLITS(1) User Commands HHBLITS(1) NAME
hhblits - fast homology detection method to iteratively search a HMM database SYNOPSIS
hhblits -i query [options] DESCRIPTION
HHblits version 2.0.15 (June 2012): HMM-HMM-based lightning-fast iterative sequence search HHblits is a sensitive, general-purpose, itera- tive sequence search tool that represents both query and database sequences by HMMs. You can search HHblits databases starting with a sin- gle 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. 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 -i <file> input/query: single sequence or multiple sequence alignment (MSA) in a3m, a2m, or FASTA format, or HMM in hhm format <file> may be 'stdin' or 'stdout' throughout. OPTIONS
-d <name> database name (e.g. uniprot20_29Feb2012) (default=) -n [1,8] number of iterations (default=2) -e [0,1] E-value cutoff for inclusion in result alignment (def=0.001) Input alignment format: -M a2m use A2M/A3M (default): upper case = Match; lower case = Insert; ' -' = Delete; '.' = gaps aligned to inserts (may be omitted) -M first use FASTA: columns with residue in 1st sequence are match states -M [0,100] use FASTA: columns with fewer than X% gaps are match states Output options: -o <file> write results in standard format to file (default=<infile.hhr>) -oa3m <file> write result MSA with significant matches in a3m format -opsi <file> write result MSA of significant matches in PSI-BLAST format -oa2m <file> write result MSA of significant matches in a2m format -ohhm <file> write HHM file for result MSA of significant matches -oalis <name> write MSAs in A3M format after each iteration -Ofas <file> write pairwise alignments of significant matches in FASTA format Analogous for output in a3m, a2m, and psi format (e.g. -Oa3m) -qhhm <file> write query input HHM file of last iteration (default=off) -seq <int> max. number of query/template sequences displayed (default=1) -aliw <int> number of columns per line in alignment list (default=80) -p [0,100] minimum probability in summary and alignment list (default=20) -E [0,inf[ maximum E-value in summary and alignment list (default=1E+06) -Z <int> maximum number of lines in summary hit list (default=500) -z <int> minimum number of lines in summary hit list (default=10) -B <int> maximum number of alignments in alignment list (default=500) -b <int> minimum number of alignments in alignment list (default=10) Prefilter options -noprefilt disable all filter steps -noaddfilter disable all filter steps (except for fast prefiltering) -nodbfilter disable additional filtering of prefiltered HMMs -noblockfilter search complete matrix in Viterbi -maxfilt max number of hits allowed to pass 2nd prefilter (default=20000) Filter options applied to query MSA, database MSAs, and result MSA -all show all sequences in result MSA; do not filter result MSA -id [0,100] maximum pairwise sequence identity (def=90) -diff [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) -cov [0,100] minimum coverage with master sequence (%) (def=0) -qid [0,100] minimum sequence identity with master sequence (%) (def=0) -qsc [0,100] minimum score per column with master sequence (default=-20.0) -neff [1,inf] target diversity of multiple sequence alignment (default=off) HMM-HMM alignment options: -norealign do NOT realign displayed hits with MAC algorithm (def=realign) -mact [0,1[ posterior probability threshold for MAC re-alignment (def=0.350) Parameter controls alignment greediness: 0:global >0.1:local -glob/-loc use global/local alignment mode for searching/ranking (def=local) -realign_max <int> realign max. <int> hits (default=1000) -alt <int> show up to this many significant alternative alignments(def=2) -premerge <int> merge <int> hits to query MSA before aligning remaining hits (def=3) -shift [-1,1] profile-profile score offset (def=-0.03) -ssm {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 -ssw [0,1] weight of ss score (def=0.11) Gap cost options: -gapb [0,inf[ Transition pseudocount admixture (def=1.00) -gapd [0,inf[ Transition pseudocount admixture for open gap (default=0.15) -gape [0,1.5] Transition pseudocount admixture for extend gap (def=1.00) -gapf ]0,inf] factor to increase/reduce gap open penalty for deletes (def=0.60) -gapg ]0,inf] factor to increase/reduce gap open penalty for inserts (def=0.60) -gaph ]0,inf] factor to increase/reduce gap extend penalty for deletes(def=0.60) -gapi ]0,inf] factor to increase/reduce gap extend penalty for inserts(def=0.60) -egq [0,inf[ penalty (bits) for end gaps aligned to query residues (def=0.00) -egt [0,inf[ penalty (bits) for end gaps aligned to template residues (def=0.00) Pseudocount (pc) options: -pcm {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) -pca [0,1] overall pseudocount admixture (def=1.0) -pcb [1,inf[ Neff threshold value for -pcm 2 (def=1.5) -pcc [0,3] extinction exponent c for -pcm 2 (def=1.0) -pre_pca [0,1] PREFILTER pseudocount admixture (def=0.8) -pre_pcb [1,inf[ PREFILTER threshold for Neff (def=1.8) Context-specific pseudo-counts: -nocontxt use substitution-matrix instead of context-specific pseudocounts -contxt <file> context file for computing context-specific pseudocounts (default=/usr/lib/hhsuite/data/context_data.lib) -cslib <file> column state file for fast database prefiltering (default=/usr/lib/hhsuite/data/cs219.lib) Predict secondary structure -addss add 2ndary structure predicted with PSIPRED to result MSA -psipred <dir> directory with PSIPRED executables (default=) -psipred_data <dir> directory with PSIPRED data (default=) Other options: -v <int> verbose mode: 0:no screen output 1:only warings 2: verbose (def=2) -neffmax ]1,20] skip further search iterations when diversity Neff of query MSA becomes larger than neffmax (default=10.0) -cpu <int> number of CPUs to use (for shared memory SMPs) (default=2) -scores <file> write scores for all pairwise comparisions to file -atab <file> write all alignments in tabular layout to file -maxres <int> max number of HMM columns (def=15002) -maxmem [1,inf[ max available memory in GB (def=3.0) EXAMPLES
hhblits -i query.fas -o query.hhr -d <database-basepath> hhblits -i query.fas -o query.hhr -oa3m query.a3m -n 1 -d <database-basepath> Download databases from ftp://toolkit.genzentrum.lmu.de/HH-suite/databases/ . hhblits 2.0.15 June 2012 HHBLITS(1)