Raccess
Raccess computes the accessibility of segment [a, b] = [x, x+l-1] in the transcript
for all the positions x with fixed length l .
prob([a, b]) = sum_{s in S[a, b]} exp(-E(s)/RT) / sum_{s in S0} exp(-E(s)/RT)
where S0 is all the possible secondary structures of the transcript
and S[a, b] is all the secondary strutures having range [a, b] as loop
region.
Thermodynamic energy that is required to keep range [a, b] being accessible
is given by
access_energy([a, b]) = -RT log(prob([a, b]))
For convenience, Raccess provides an option (-bind_range)
to computes the binding energy with a complementary DNA fragment
in the accessible region.
<- -> bind range
__________
a |||||||||| b
------------|---------------------|----------
(( )) () () () ()
Usage:
run_raccess [options]
option:
-seqfile=<fasta file> : input sequences in fasta format.
-access_len=<integer> : contiguous length over which
the transcript is accesible [default: 50]
-outfile=<directory> : output directory [default: ./]
-bind_range=<first>:<last> : for each segment of accessibility computation,
the binding energy between the region [first, last]
(in 1-based, inclusive-end, coordinates
relative to the segment)
with a complementary DNA/RNA fragment
is calculated [default: none]
-bind_dna=<bool> : if true, binding energy is computed for a
complementary DNA fragment
if false, binding energy is computed
for a complementary RNA fragment. [default: true]
-max_span=<integer> : maximal span of base pairs considered [default: 100]
-energy_thr=<double> : only output the results below the
specified energy threshold (unit: kcal/mol) [default: 100]
Output:
file: outdir/raccess_out.txt
>fasta_header
pos1 len1,ene11;len2,ene12;
pos2 len1,ene21;len2,ene22;
field description:
pos : sequence position x in 0-based coordinate
accessibility of the range [x, x + access_len - 1] is computed
len: access_len
ene: free energy to access in this region calculated from the formula:
energy [kcal/mol] = - RT log(probability) with RT=0.61633008[kcal/mol]
There is a new line at the end of each fasta sequence.
Example:
./src/raccess/run_raccess -outfile=./example/raccess_out.txt -seqfile=./example/dna.fa -access_len=5,10,20 -max_span=80
raccess_out.txt
----------------------------------------
>AB000263
350 5,0.587571;
349 5,0.671838;
348 5,0.688657;
347 5,0.632836;
346 5,0.632803;
345 5,0.742851;10,0.856473;
344 5,0.761075;10,0.867324;
343 5,1.05019;10,1.15432;
342 5,0.906549;10,1.16339;
341 5,0.674628;10,1.10179;
340 5,0.563941;10,1.21421;
339 5,0.7748;10,1.43912;
338 5,0.855941;10,1.46161;
337 5,1.50655;10,1.81358;
336 5,1.77874;10,2.04356;
335 5,1.78954;10,1.86431;20,2.0987;
334 5,2.6894;10,2.77606;20,3.01488;
333 5,3.38362;10,3.46585;20,3.71417;
332 5,3.39939;10,3.49725;20,3.74974;
331 5,2.55136;10,3.46097;20,3.74418;
330 5,2.7096;10,3.67404;20,3.98726;
329 5,2.84122;10,3.8007;20,4.13477;