hhalign - align a query alignment/HMM to a template
alignment/HMM
hhalign -i query -t template [options]
HHalign 3.3.0 Align a query alignment/HMM to a template
alignment/HMM by HMM-HMM alignment If only one alignment/HMM is given it is
compared to itself and the best off-diagonal alignment plus all further
non-overlapping alignments above significance threshold are shown.
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. BMC Bioinformatics, doi:10.1186/s12859-019-3019-7 (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
- -t <file>
- input/template: 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.
- -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)
- -o <file>
- write results in standard format to file (default=<infile.hhr>)
- -oa3m
<file>
- write query alignment in a3m or PSI-BLAST format (-opsi) to file
(default=none)
- -aa3m
<file>
- append query alignment in a3m (-aa3m) or PSI-BLAST format
(-apsi )to file (default=none)
- -Ofas
<file>
- write pairwise alignments in FASTA xor A2M (-Oa2m) xor A3M
(-Oa3m) format
- -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
- -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=0)
- -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=100)
- -z <int>
- minimum number of lines in summary hit list (default=1)
- -B <int>
- maximum number of alignments in alignment list (default=100)
- -b <int>
- minimum number of alignments in alignment list (default=1)
Filter options applied to query MSA, template MSA, and 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 Zero and non-numerical
values turn off the filtering. (def=100)
- -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)
- -mark
- do not filter out sequences marked by ">@"in their name
line
- -norealign
- do NOT realign displayed hits with MAC algorithm (def=realign)
- -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
- -excl
<range>
- exclude query positions from the alignment, e.g. '1-33,97-168'
- -template_excl
<range>
- exclude template positions from the alignment, e.g. '1-33,97-168'
- -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=1)
- -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}
- secondary structure scoring [default=2]
- 0:
- = no ss scoring
- 1,2:
- = ss scoring after or during alignment
- 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!
- -gapb [0,inf[
- Transition pseudocount admixture (def=1.00)
- -gapd [0,inf[
- Transition pseudocount admixture for open gap (default=0.15)
- -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 the gap open penalty for deletes (def=0.60)
- -gapg ]0,inf]
- factor to increase/reduce the gap open penalty for inserts (def=0.60)
- -gaph ]0,inf]
- factor to increase/reduce the gap extend penalty for
deletes(def=0.60)
- -gapi ]0,inf]
- factor to increase/reduce the 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)
- 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 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)
- -v <int>
- verbose mode: 0:no screen output 1:only warings 2: verbose (def=2)
- -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)
Example: hhalign -i T0187.a3m -t d1hz4a_.hhm
-o result.hhr