hyfi-sieve

Description: Reports all k-mers that could could anchor genomic binding sites for DNA sequence queries.

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

Input:

• <FASTA file>: A FASTA file with at least one sequence.  If a '-' is given instead of a filename, then sieve-kmers attempts to read from standard input.

Output: A FASTA file whose sequences are all k-mers.  Each reported k-mer could anchor genomic binding sites for the sequences queries.  For each k-mer, there is a space-delimited header line with the following fields:

>kmer-id <space> qid:query id <space> qs:query sequence <space> fmm:mismatch filter val <space> fth:thermo filter val <space> fal: alignment filter val <space> fdg: dg filter val
All output is written to standard output.

Options:

• -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 the standard out.
• -p <parameter filename>: use the parameters in the specified file, rather than the internal thresholds calibrated for identifying binding sites at 55 C in 50 mM NaCl and 2 mM MgCl₂.  The parameter file can be made with the program hyfi-parameters.
• -v <number>: verbosity level. The verbosity is controlled by <number>; 0 means no extra output, and 5 means extreme verbosity. The default is 0.
• -d <number>: directory containing thermodynamic parameters.
• --characterize-filters <filename>: analyze the performance of the k-mer filters, and write the results to the specified file.

Bugs: None reported yet.