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500.conf
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# This is the configuration file for single-sequence SQUARNA to be run on sequence longer than 500nts
# A name of a parameter set should be in a separate line starting with ">" symbol
# The first parameter set in a config file must include all the parameters listed
# For any of the following parameter sets the values of the first set will be used by default unless they are overwritten
# This config file includes five parameter sets named 500G1, 500G2, defN, defE, and defH
# Everything in a line after a "#" symbol is ignored by the tool
# Empty lines are also ignored
>500G1
algorithms G # comma-separated list; G - Greedy; N - Nussinov; H - Hungarian; E - Edmonds
bpp 0
bpweights GC=3.25,AU=1.25,GU=-1.25 # List of allowed base pairs and their scores
suboptmax 0.95 # Final range to keep suboptimal stems
suboptmin 0.9 # Starting range to keep suboptimal stems
suboptsteps 1 # Number of events of suboptimal stems being kept to reach suboptmax from suboptmin
minlen 2 # Minimum stem length
minbpscore 4.5 # Minimum raw stem score (sum of bp weights, by default equals to 1GC+1AU)
minfinscorefactor 1.25 # Factor to calculate the minimum corrected stem score (the score is minbpscore*minfinscorefactor)
# The corrected stem score: corrscore = bpscore * distfactor * orderfactor * loopfactor * tetraloopbonus
# distfactor = (1 / (1 + abs(stemdist - idealdist))) ^ distcoef
# idealdist = 4 if hairpin and 2 otherwise
# stemdist = #dots + #brackets * bracketweight
# orderfactor = (1 / (1 + order)) ^ orderpenalty
# order = stems of how many orders are in conflict with the current stem
# loopfactor = 1 + loopbonus*[inner loop is good]*symfactor1 + loopbonus*[outer loop is good]*symfactor2
# a good loop is a short near-symmetric internal loop like (1, 2), (4, 4), etc.
# symfactor is 2.0 for symmetric loops, 1.5 for (x-1, x) loops, and 1.0 for (x-2, x) loops
# tetraloopbonus is 1.25 for confined GNRA tetraloops and 1.0 for everything else
distcoef 0.09 # a higher value gives higher priority to short-range stems
bracketweight -2 # values close to -2 balance a high orderpenalty to some extent
orderpenalty 1.0 # a higher value gives higher penalty to pseudoknots according to their order
loopbonus 0.125 # bonus for short near-symmetric internal loops (from each side of the stem)
maxstemnum 1e6 # Maximum number of stems to be predicted for a single structure
>500G2
bpweights GC=2,AU=1,GU=1
minbpscore 3
minfinscorefactor 0.99
distcoef 0.1
orderpenalty 1.35
>defN
algorithms N
bpweights GC=3.5,AU=1,GU=-1
minlen 2
minbpscore 2.75
>defE
algorithms E
bpweights GC=3.75,AU=1.75,GU=0.5
minlen 2
minbpscore 4.5
>defH
algorithms H
bpweights GC=3.75,AU=1.75,GU=0.5
minlen 2
minbpscore 4.5