hyfi-parameters

Description: Analyzes a set of binding sites to determine filter thresholds.

Usage:hyfi-parameters [options] <FASTA file>

Input:

• <FASTA file>: A FASTA file with queries and binding sites. If a '-' is given instead of a filename then standard input is read. The header files must provide information about the parameters used for the binding site search, and the query sequence that binds to the sequences in the FASTA file.  The first fild provides information about the location of the binding site. In particular, the headers must be structured as follows:

> sequence id:start-stop:strand <space> qid:query id <space> qs:query sequence <space> dg:delta G <space> na:naconc <space> mg:mgconc <space> t:temperature

Output: Hyfi search parameters in a format where each line contains a key, a colon, and then a value. All output is written to standard output by default.

Options:

• --dg-delta <number>: Pass all binding sites whose binding energy to the query is within the delta of the binding energy of the query to itself.
• --dg-max <number>: maximum delta G to analyze; defaults to -7 kcal/mole
• --use-mismatch-filter <1|0>: defaults to 1; if 0, the mismatch filter is not used
• --use-thermodynamic-filter <1|0>: defaults to 1; if 0, the mismatch filter is not used
• --use-alignment-filter <1|0>: defaults to 1; if 0, the mismatch filter is not used
• --use-deltag-filter <1|0>: defaults to 1; if 0, the mismatch filter is not used
• -k <number>: the length of k-mer to index; defaults to 10.
• -d <number>: directory containing thermodynamic parameters.
• -o <output filename>: write the program output to an output file, rather than the standard out.
• -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.