hyfi-scan
Description: Scans a genome for sequence binding sites using Zuker's hybrid software.
Usage:
hyfi-scan [options] <FASTA filename> <sequence file>
Input:
- <FASTA filename>: A FASTA file with query sequences. If the FASTA filename is '-', then standard input is read.
- <sequence file>: a FASTA format sequence file with one sequence entry.
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:
- --window-length <length>: compute delta G for a sequence window of <length> bases.
- --na-conc <number>: sodium concentration in units of moles per liter; defaults to .050
- --RNA: do scan using RNA thermodynamics
- -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.
- --mg-conc <number>: magnesium concentration in units of moles per liter; defaults to .002
- --temp <number>: temperature in celsius; defaults to 55 C.
- --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.
- --start <number>: start scanning at the specified fasta record in the file; by default, all records are scanned
- --stop <number>: stop scanning at the specified fasta record in the file; by default, all records are scanned
- -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.