hyfi-filter

Description: Filters a list of candidate binding partners for a query sequence using an accurate model of DNA binding affinity.

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

Input:

• <FASTA file>: A space-delimited file of sequences and candidate binding partners. If a '-' is given instead of a filename, then standard input is read. Each candidate binding sequence in the FASTA file must be accompanied by the following header information:
  

> seq id:start-stop:strand <space> qid:query id <space> qs:query sequence

If no sequence file is given, then dg-filter attempts to read the standard input.

Output: A FASTA file with delta G and hybridization condition information appended to the header file. The delta G is computed for each sequence and the query sequence in the header. All output is written to standard output. Each output header is formatted 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

Options:

• --dg-max <number>: pass all pairs that bind with at least the specified affinity, in units of kilocalories per mole. This defaults to -7 kilocalories per mole.
• --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.
• -o <filename>: write output to the specified file, instead of the standard out.
• -d <number>: directory containing thermodynamic parameters.
• -p <parameter file>: use parameters from the parameter file to modify search for custom hybridization conditions.
• -v <number>: verbosity level. The verbosity is controlled by <number>; 0 means no extra output, and 5 means extreme verbosity. The default is 0.