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 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

HMM-HMM alignment options:¶

-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!

Gap cost options:¶

-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)

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 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)

-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