ffindex_from_fasta(1) [debian man page]
FFINDEX_FROM_FASTA(1) User Commands FFINDEX_FROM_FASTA(1) NAME
ffindex_from_fasta - populate index from FASTA file DESCRIPTION
USAGE: ffindex_from_fasta -v | [-s] data_filename index_filename fasta_filename -s sort index file ENVIRONMENT FFINDEX_MAX_INDEX_ENTRIES - allocate memory for this number of entries Designed and implemented by Andreas W. Hauser <hauser@genzentrum.lmu.de>. BUGS
User feedback is welcome, especially bugs, performance issues and last but not least convenience of the programs and API. Email Andreas Hauser hauser@genzentrum.lmu.de. ffindex_from_fasta version 0.96, off_t = 64 bits June 2012 FFINDEX_FROM_FASTA(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)