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:
- <sequence filename>: A tab delimited file, where each line has three fields, in the following order: an ID, a DNA sequence, and finally another DNA sequence. The two DNA sequences are assumed to be PCR primers. If the sequence filename is '-', then standard input is read.
- <sequence file>: a FASTA format sequence file
- <index file>: an index into the fasta file
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:
- --window-length <length>: compute delta G for a sequence window of <length> bases.
- -p <parameter file>: use parameters from the parameter file to modify search for custom hybridization conditions.
- -d <number>: directory containing thermodynamic parameters.
- -o <output filename>: write the program output to an output file, rather than the standard out.
- --dg-max <number>: maximum delta G to report; 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.
- --max-separation <number>: Maximum separation between two cooperating binding sites; defaults to 1000 bases.
- -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.