hyfi-scan

Description: Scans a genome for sequence binding sites using Zuker's hybrid software.

Usage: hyfi-scan [options] <FASTA filename> <sequence file>

Input:

Output:A FASTA file with sequences that will bind to the queries with better than a specified affinity. The header for each sequence contains first an identifier for the binding site sequence, and then space delimited fields with more information. The identifier specifies where to find the binding site sequence, and is formatted like this:"seq id:start-stop:strand". Following are space-delimited fields more fully explained in this glossary .

> 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:

Bugs: None reported yet.