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)