Provided by: hhsuite_3.0~beta3+dfsg-3_amd64 bug

NAME

       hhblits - fast homology detection method to iteratively search a HMM database

SYNOPSIS

       hhblits -i query [options]

DESCRIPTION

       HHblits 3.0.0 (15-03-2015): 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.

       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) Multiple databases may be specified with
              '-d <db1> -d <db2> ...'

       -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

       -tags/-notags
              do NOT / do neutralize His-, C-myc-, FLAG-tags, and trypsin recognition sequence to
              background distribution (def=-notags)

   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

       -ohhm <file>
              write HHM file for result MSA of significant matches

       -oalis <name>
              write MSAs in A3M format after each iteration

       -add_cons
              generate consensus sequence as master sequence of query MSA (default=don't)

       -hide_cons
              don't show consensus sequence in alignments (default=show)

       -hide_pred
              don't show predicted 2ndary structure in alignments (default=show)

       -hide_dssp
              don't show DSSP 2ndary structure in alignments (default=show)

       -show_ssconf
              show confidences for predicted 2ndary structure in alignments

       -Ofas <file>
              write pairwise alignments in FASTA xor A2M (-Oa2m) xor A3M (-Oa3m) format

       -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)

       -maxfilt
              max number of hits allowed to pass 2nd prefilter (default=20000)

       -min_prefilter_hits
              min number of hits to pass prefilter (default=100)

       -prepre_smax_thresh
              min score threshold of ungapped prefilter (default=10)

       -pre_evalue_thresh
              max E-value threshold of Smith-Waterman prefilter score (default=1000.0)

       -pre_bitfactor
              prefilter scores are in units of 1 bit / pre_bitfactor (default=4)

       -pre_gap_open
              gap open penalty in prefilter Smith-Waterman alignment (default=20)

       -pre_gap_extend
              gap extend penalty in prefilter Smith-Waterman alignment (default=4)

       -pre_score_offset
              offset on sequence profile scores in prefilter S-W alignment (default=50)

       Filter options applied to query MSA, database MSAs, and result MSA

       -all   show all sequences in result MSA; do not filter result MSA

       -interim_filter NONE|FULL

              filter sequences of query MSA during merging to avoid early stop (default: FULL)

              NONE: disables the intermediate filter FULL: if an early stop occurs compare filter
              seqs in an all vs. all comparison

       -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 Zero and non-numerical values turn off the
              filtering. (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)

       -mark  do not filter out sequences marked by ">@"in their name line

   HMM-HMM alignment options:
       -norealign
              do NOT realign displayed hits with MAC algorithm (def=realign)

       -realign_old_hits
              realign hits from previous iterations

       -mact [0,1[
              posterior prob threshold for MAC realignment controlling  greediness  at  alignment
              ends: 0:global >0.1:local (default=0.35)

       -glob/-loc
              use global/local alignment mode for searching/ranking (def=local)

       -realign
              realign displayed hits with max. accuracy (MAC) algorithm

       -realign_max <int>
              realign max. <int> hits (default=500)

       -ovlp <int>
              banded alignment: forbid <ovlp> largest diagonals |i-j| of DP matrix (def=0)

       -alt <int>
              show up to this many alternative alignments with raw score > smin(def=4)

       -smin <float>
              minimum raw score for alternative alignments (def=20.0)

       -shift [-1,1]
              profile-profile score offset (def=-0.03)

       -corr [0,1]
              weight of term for pair correlations (def=0.10)

       -sc    <int>          amino acid score         (tja: template HMM at column j) (def=1)

       0      = log2 Sum(tja*qia/pa)   (pa: aa background frequencies)

       1      = log2 Sum(tja*qia/pqa)  (pqa = 1/2*(pa+ta) )

       2      = log2 Sum(tja*qia/ta)   (ta: av. aa freqs in template)

       3      = log2 Sum(tja*qia/qa)   (qa: av. aa freqs in query)

       5      local amino acid composition correction

       -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)

       -ssa [0,1]
              ss confusion matrix = (1-ssa)*I + ssa*psipred-confusion-matrix [def=1.00)

       -wg    use global sequence weighting for realignment!

   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:
              Context specific hhm pseudocounts:

       -pc_hhm_contxt_mode {0,..,3}
              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) 3: CSBlast admixture:   tau =
              a(1+b)/(Neff[i]+b) (Neff[i]: number of effective seqs in local MSA around column i)

       -pc_hhm_contxt_a
              [0,1]        overall pseudocount admixture (def=0.9)

       -pc_hhm_contxt_b
              [1,inf[      Neff threshold value for mode 2 (def=4.0)

       -pc_hhm_contxt_c
              [0,3]        extinction exponent c for mode 2 (def=1.0)

              Context  independent hhm pseudocounts (used for templates; used for query if contxt
              file is not available):

       -pc_hhm_nocontxt_mode {0,..,3}
              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)

       -pc_hhm_nocontxt_a
              [0,1]        overall pseudocount admixture (def=1.0)

       -pc_hhm_nocontxt_b
              [1,inf[      Neff threshold value for mode 2 (def=1.5)

       -pc_hhm_nocontxt_c
              [0,3]        extinction exponent c for mode 2 (def=1.0)

              Context specific prefilter pseudocounts:

       -pc_prefilter_contxt_mode {0,..,3}
              position dependence of pc admixture 'tau' (pc mode, default=3)

       0: no pseudo counts:
              tau = 0

       1: constant
              tau = a

              2: diversity-dependent: tau = a/(1+((Neff[i]-1)/b)^c) 3: CSBlast admixture:   tau =
              a(1+b)/(Neff[i]+b) (Neff[i]: number of effective seqs in local MSA around column i)

       -pc_prefilter_contxt_a
              [0,1]        overall pseudocount admixture (def=0.8)

       -pc_prefilter_contxt_b
              [1,inf[      Neff threshold value for mode 2 (def=2.0)

       -pc_prefilter_contxt_c
              [0,3]        extinction exponent c for mode 2 (def=1.0)

              Context independent prefilter pseudocounts (used if context file is not available):

       -pc_prefilter_nocontxt_mode {0,..,3}
              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)

       -pc_prefilter_nocontxt_a
              [0,1]        overall pseudocount admixture (def=1.0)

       -pc_prefilter_nocontxt_b
              [1,inf[      Neff threshold value for mode 2 (def=1.5)

       -pc_prefilter_nocontxt_c
              [0,3]        extinction exponent c for mode 2 (def=1.0)

              Context-specific pseudo-counts:

       -nocontxt
              use substitution-matrix instead of context-specific pseudocounts

       -contxt    <file>    context    file    for    computing   context-specific   pseudocounts
              (default=./data/context_data.crf)

       -csw   [0,inf]  weight of central position in cs pseudocount mode (def=1.6)

       -csb   [0,1]    weight decay parameter for positions in cs pc mode (def=0.9)

   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=20.0)

       -cpu <int>
              number of CPUs to use (for shared memory SMPs) (default=2)

       -scores <file> write scores for all pairwise comparisons to file

       -filter_matrices filter matrices for similarity to output at most 100 matrices

       -atab  <file> write all alignments in tabular layout to file

       -maxres <int>
              max number of HMM columns (def=20001)

       -maxmem [1,inf[ limit memory for realignment (in GB) (def=3.0)

EXAMPLES

       hhblist -i query.fas -o query.hhr -d ./uniclust30

       hhblits -i query.fas -o query.hhr -oa3m query.a3m -n 1 -d ./uniclust30

       Download                                  databases                                   from
       <http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/>.