## 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