hyfi: software suite for binding site search
This collection of software is designed to rapidly identify binding sites for a query sequence in genomic DNA. It implements an approach described in an upcoming paper by Tobias Mann and William Stafford Noble. This software suite has four main programs:
There are also some utilites referenced at the end of this overview. This software is implemented in C. Instructions for obtaining the software will be forthcoming.
- A program for indexing a sequence file to speed up the binding site search.
- A program for retrieving the binding sites of a query sequence.
- A program for identifying sites where PCR primers could co-operate to exponentially amplify a sequence
- A program for analyzing a set of binding sites to tailor the search for different reaction conditions.
Indexing a sequence file to speed up the binding site search.Our approach requires the pre-computation of an index into a sequence file. Here is an example command line for building an index on a sequence file:
hyfi-index chr22.fa chr22.idx
Here is more documentation on the program used for indexing sequence files:
Retrieving binding sites for a queryMost of the time, binding partner searches will be done with the program hyfi. Here is an example command line for the standard binding partner search:
hyfi query.fasta chr22.fa chr22.idx
The command above will produce a complete list of the sites that will bind to the query sequences in the genomic DNA of interest. Here is more information about hyfi:
PCR primer analysisThe binding partner search for PCR, where the focus is on cooperating primers rather than binding sites per se is handled by
hyfi-cooperative-search. Here is an example command line for searching for co-operating PCR primers:
hyfi-cooperative-search primer-file chr22.fa chr22.idx
The command above will identify all sequences in chr22.fa such that two primers in primer-file could bind to produce a PCR product. Here is more information about
Analyzing a set of binding sites to customize the search for different reaction conditionsBecause hybridization experiments are done in a wide range of conditions, we include software for tailoring the search criteria for particular salt and temperature conditions. By default, we assume that hybridization is done at 55 C in 50 mM NaCl and 2 mM MgCl2 (defaults were chosen for similarity to PCR annealing conditions). Here is an example command line for obtaining parameters more appropriate for finding the binding partners of a query in high salt (i.e. 1 M NaCl) and low temperature (37 C) conditions:
hyfi-scan -naconc 1 -temp 37C test-sequences.txt chr22.fa | hyfi-parameters > 1_M_salt.params
The binding site searches above would then be modified slightly:
hyfi -p 1_M_salt.params query.fasta chr22.fa chr22.idx
Here is documentation for the binding site analysis programs.
Other utilitiesHyfi has a set of utilities as well.