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]
  -outdir=<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_pair_dist=<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
	field description:
	  pos          :  sequence position x in 1-based coordinate
                          accessibility of the range [x, x + access_len - 1] is computed
          access_energy:  free energy to access in this region calculated from the formula: 
                          energy [kcal/mol] = - RT log(probability)
          bind_energy  :  binding energy with complemantary DNA fragment
                          in the region [fist, last] set by -bind_range option
			  (only output when -bind_range is set)
          tot_energy   :  shows (access_energy + bind_energy) 
	                  (only output when -bind_range is set)

        Types of fields are described in the first row of the output file.
	If neither -bind_energy nor -print_prob is set,
         then only pos, and access_energy fields are displayed.
        If -bind_range is set,
	 then bind_energy, and tot_energy fields are added to each row.

Example:
run_raccess.exe -seqfile=example/dna.fa -bind_range=1:7 
		   
raccess_out.txt
----------------------------------------
#pos	acc_energy	bind_energy	tot_energy
>AB000263
1	0.0057257	-5.8	-5.79427
2	0.00572568	-5.2	-5.19427
3	0.00550336	0	0.00550336
4	0.00550327	0	0.00550327
5	0.00550299	0	0.00550299
6	0.00502714	0	0.00502714
7	0.00502678	0	0.00502678
8	0.00480352	0	0.00480352
9	1.27273e-014	0	1.27273e-014
10	1.38221e-014	0	1.38221e-014
11	1.4917e-014	0	1.4917e-014
12	1.60118e-014	0	1.60118e-014
13	1.71066e-014	0	1.71066e-014
14	1.82014e-014	0	1.82014e-014
15	0.80193	0	0.80193
16	0.86845	0	0.86845