hyfi-cooperative-search

Description: Scans a sequence for cooperating binding sites (sites such that two primers could generate an exponentially amplified PCR product) using Zuker's hybrid software.

Usage: hyfi-cooperative-search [options] <sequence filename> <sequence file> <index file>

Input:

Output: A FASTA file with sequences to which both primers from a line of the input could bind to produce undesired amplification: one primer sequence will have affinity for the reverse complement of the sequence at the 5' end, and one primer sequence will have affinity for the 3' end. These two sequences will not necessarily be different.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.

> sequence id:start-stop:strand <space> ppid: ID of the primer pair sequence <space> pf: forward primer sequence (binding to RC of 5' region of sequence) <space> pr: reverse primer sequence (binding to 3' region of sequence) <space> pfdg:delta G of forward primer binding site <space> prdg:delta G of reverse binding site <space> na:naconc <space> mg:mgconc <space> t:temperature

All output is written to standard output.

Options:

Bugs: None reported yet.