hyfi

Description: Reports all binding sites for query sequences in genomic DNA, according to an accurate model of DNA hybridization.

Usage: hyfi [options] <FASTA query file> <FASTA sequence file> <index file>

Input:

• <FASTA query file>: A FASTA file with at least one sequence. If the filename is a '-', then hyfi attempts to read from standard input.
• <FASTA sequence file>: A FASTA file with the sequence to be searched.
• <index file>: A file with an index into the search sequence, made with hyfi-index

Output: A list of binding sites for each query sequence in FASTA format.  Each sequence in the output FASTA file contains a binding site for one of the queries.  The header for each sequence contains first an identifier for the binding site sequence, and then space delimited fields with more information 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

All output is written to standard output.

Options:

• -c: include only the window centered on the k-mer, rather than all windows including the k-mer
• --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.
• --window-length <window size>: for each position, return a subsequence including <window size> bases; defaults to 30.
• -d <number>: directory containing thermodynamic parameters.
• -p <parameter file>: use parameters from the specified parameter file to modify the search for custom hybridization conditions.
• -s: sieve one sequence specified on the command line, rather than a file of sequences.
• -o <filename>: write output to the specified file, instead of standard output.
• --characterize-filters <filename>: analyze the performance of the filters, and write the results to the specified file.
• -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.