## COMER/COTHER options
##
[OPTIONS]
## Output options:
##
# Print hits with e-value below this value [Real]
EVAL = 10.0
# Number of hits to show in the result list [Integer]
NOHITS = 700
# Number of alignments to show in the output [Integer]
NOALNS = 700
# Show statistical parameters below alignments (0|1)
SHOW = 1
# Maximum length of description lines; [Integer]
# smaller values reduce memory requirements
DSCLEN = 1024
# Width to wrap description lines during output [40-100000]
DSCWIDTH = 80
# Width to wrap alignments during output [20-100000]
ALNWIDTH = 60
## Profile construction options:
##
# Make profile positions masked with Xs (0|1)
# uninformative
X_UNINF = 1
# Ignore sequences in alignment file with this or [1-100]
# higher level of sequence identity
IDENTITY = 90
# Include the command line text in the profile (0|1)
# (NOTE: occupies additional disk space)
SHOWCMD = 0
## ADVANCED options
##
## Profile construction options:
##
# Weight for pseudocount frequencies [Real]
PCFWEIGHT = 1.5
# Minimum fraction (percentage) of alignment an [1-100]
# extent must cover
MINALNFRN = 5
# Minimum number of alignment positions an [Integer]
# extent must consist of (comb. with MINALNFRN)
MINALNPOS = 10
# Initial amino acid substitution matrix: [Choice]
# Blosum80 -- BLOSUM 80% matrix
# Blosum62 -- BLOSUM 62% matrix
# Blosum45 -- BLOSUM 45% matrix
# Pscores -- locally constructed matrix
# Gonnet -- Gonnet matrix
SUBMAT = Gonnet
## Position-specific distance distribution options:
##
# Indivisible fragment of consecutive distance [1-20]
# values in dynamic programming when calculating
# similarity between two distance distributions
# (programs: adddist, cother)
DSTSEGM = 6
# Number of positions in sequence used as the [1-20]
# threshold for penalizing missing values (below)
# (programs: adddist)
DSTNPOS = 12
# Distance penalty in Angstroms for missing [1-64]
# values in a region separated by less than
# DSTNPOS positions in sequence from the main
# diagonal
# (programs: adddist)
DSTSEP6 = 12
# Distance penalty in Angstroms for a long [1-255]
# gap of missing values of a length of more
# than DSTNPOS positions in sequence from the
# main diagonal; a value of 255 translates to a
# negative score
# (programs: adddist)
DSTGAPL = 24
# Number of positions from the main diagonal [1-20]
# defining the distance processing-free band
# (programs: adddist)
DSTFREE = 3
## Cluster data usage:
##
# Score adjustment
# hdpctx -- within statistical framework of HDP
# hdpsco -- using scores derived from HDP cluster
# distribution along structural alignments
# no -- do not apply score adjustment
SCOADJ = hdpsco
# Number of support clusters to use (-1: all) [Integer]
SUPCLT = 5
# Weight of adjusted scores (0.-1.)
ADJWGT = 0.33
# Weight for auxiliary scores (0.-1.)
cADJWGT = 0.33
## Distance distribution match scores
##
# Weight of match scores (0 -- disables them) [0.-1.)
DDMSWGT = 0.2
## Normal vector scores
##
# Weight of vector scores (0 -- disables them) [0.-1.)
CVSWGT = 0.15
## SS scores:
##
# Weight of SS scores [0.-1.)
# (0 -- disables both SSSWGT and SSSHDP)
# (in effect only if profiles include SS prediction)
SSSWGT = 0.12
## Statistical significance estimation
##
# Index of a model for the estimation of statistical (0|1|2)
# significance
# (0 -- significance depends on profile lengths)
# (1 -- significance depends on profile attributes
# and compositional similarity)
# (2 -- same as model 1 but regards the amount of
# data used in simulations)
SSEMODEL = 2
## SEG options:
##
# Invoke high-complexity filter in alignment (0|1)
# columns
HCFILTER = 0
# Window length [Integer]
HCWINDOW = 12
# Low entropy threshold [Real]
HCLOWENT = 3.3
# High entropy threshold [Real]
HCHIGHENT = 3.4
# Invoke low-complexity filtering of query (0|1)
INVLCFILTER = 0
# Invoke LC filtering for each sequence in (0|1)
# alignment using same parameters below
LCFILTEREACH = 1
# Window length [Integer]
LCWINDOW = 8
# Low entropy threshold [Real]
LCLOWENT = 1.6
# High entropy threshold [Real]
LCHIGHENT = 1.6
# Distance of equivalence between profile vectors [Real]
DISTANCE = 12.96
## Alignment options:
##
# Realign alignments by a maximum a posteriori (0|1)
# algorithm
MAPALN = 1
# Posterior probability threshold in calculating [0-1)
# expected alignment accuracy when MAPALN = 1;
# 0 -- maximally extended alignments;
# NOTE: values tending to 1 shorten alignments
MINPP = 0.28
## -------------------------------------------------------------------
## COMER web service options
##
## COMER profile database
comer_db = pdb70_201014
## COTHER profile database
cother_db = pdb70_210614
## Sequence database to use for profile construction
## (blank if not in use)
sequence_db = uniref50.fasta
## HHsuite database to use for profile construction
## (blank if not in use)
hhsuite_db = UniRef30_2020_03
## Flag of using HHsuite for profile construction
## (0 if not to be used)
hhsuite_in_use = 1
## Options for HHsuite: number of iterations
hhsuite_opt_niterations = 2
## Options for HHsuite: E-value threshold
hhsuite_opt_evalue = 1.e-3
## Flag of using HMMER for profile construction
## (0 if not to be used)
hmmer_in_use = 1
## Options for HMMER: number of iterations
hmmer_opt_niterations = 2
## Options for HMMER: E-value threshold
hmmer_opt_evalue = 1.e-3
## KEY required by the Modeller software
modeller_key = MODELLERKEY
## Flag of modeling multiple query fragments using all
## pairs listed in the (input) file of pairwise
## alignments
model_all_pairs = 0