hyfi-pairwise-deltag

Description: Computes all pairwise delta G values for a set of sequences using Zuker's hybrid software, and writes the result to a tab delimited matrix.

Usage: hyfi-pairwise-deltag [options]

Output: A tab delimited file containing a matrix of delta G values. Each row and column is associated with a sequence, and the entry in a particular row and column contains the delta G of the sequence associated with the row binding to the reverse complement of the sequence associated with the column. Each row and column is labelled with a sequence; the first row consists of column labels, and each row begins with a label.

All output is written to standard output.

Options:

• -k <number>: compute the matrix for all k-mers of the specified length. This is the default operation, and k defaults to 4.
• -f <input FASTA filename>: compute the pairwise delta G for the sequences in the FASTA file; if <input FASTA filename> is a '-' then hyfi-pairwise-deltag attempts to read standard input.
• -d <number>: directory containing thermodynamic parameters.
• -o <output filename>: write the program output to an output file, rather than the standard out.
• --na-conc <number>: sodium concentration in units of moles per liter; defaults to .05
  
• --mg-conc <number>: magnesium concentration in units of moles per liter; defaults to .002
• --temp <number>: temperature in celsius; defaults to 55 C.
• -v <number>: verbosity level. The verbosity is controlled by <number>; 0 means no extra output, and 5 means extreme verbosity. The default is 0.

Bugs: None reported yet.