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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 3.1.0: 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.

Steinegger M, Meier M, Mirdita M, V??hringer H, Haunsberger S J, and S??ding J (2019) HH-suite3 for fast remote homology detection and deep protein annotation. bioRxiv, 560029. doi:10.1101/560029 (c) The HH-suite development team

-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

-blasttab <name> write result in tabular BLAST format (compatible to -m 8 or -outfmt 6 output)

1
2 3 4 5 6 8 9 10 11 12
'query target #match/tLen #mismatch #gapOpen qstart qend tstart tend eval score'
-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=)

-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
-maxseq <int>
max number of input rows (def=65535)
-maxres <int>
max number of HMM columns (def=20001)

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

EXAMPLES

hhblits -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/>.

July 2019 hhblits 3.2.0