Installation

For installation instructions, please refer to the file Installation.md.

Usage

After building and installing the BindoligoNet programs, the general form for running them is:;

  bindoligo <options> [s sequence] [t sequence]

or, for DNA-DNA pairings, with:

  bindoligo-D <options> [s sequence] [t sequence]

Both the s and t sequences can be provided by specifying the path of a file or by specifying the sequence directly on the command line. To specify files for s and t, use switches

  -s <s_file> -t <t_file>

Each file should have one sequence per line and should consist exclusively of A, C, G, U, and T characters (case insensitive). In all cases, sequences should be entered 5' -> 3'. Note that sequences entered explicitly on the command line must be provided following all flags.

BindoligoNet can be run in either single mode (accepting two sequences) or batch mode. The mode is specified with the -m switch:

  -m s (single, default)
  -m b (batch)

There are two ways of using batch mode: one s to many t's, or n s's to n t's. For one s with many t's, s must be specified on the command line, and t given as a file. For example:

 -m b -t targets.txt acgugaugaugac

In the latter case, both must be specified as files of equal length:

  -m b -s oligos.txt -t targets.txt

BindoligoNet can report optimal alignments, MFEs, or the free energy landscape dG(j). Output is selected with the mandatory -o switch.

  -o a (optimal alignment)
  -o d (MFE)
  -o l (energy landscape)

To facilitate automation, BindoligoNet can output to a file, specified with the -f switch. If this option is omitted, BindoligoNet defaults to printing to standard output.

  -f <file> (if omitted, outputs to stdout)

BindoligoNet can implement all secondary structure removal penalty schemes detailed in the paper (dG_5, dG_2, dG_0). In addition, it is possible to enter custom 5 parameter or 2 parameter models.

 -P 5 (dG_5, default)
 -P 2 (dG_2)
 -P 0 (dG_0)
 -P C (custom 5 parameter)
 -P c (custom 2 parameter)

If custom 5-parameter (-P C) or custom 2-paarmeter (-P c) options are used, parameters are specified using the -C flag:

 -P C -C g0,gA,gC,gG,gU
 -P c -C g0,gL

Examples

bindoligo -m s -o a ccccccc ggggggggggg

will output the optimal alignment between the sequences s=ccccccc and t=ggggggggggg.

bindoligo -m b -o d -t targets.txt uacuuaccuggc

will output a list of MFEs from pairing the given oligo (uacuuaccuggc) to each sequences in the file targets.txt.