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 a paper by Tobias Mann and William Stafford Noble ( Efficient identification of DNA hybridization partners in a sequence database ).  This software suite has four main programs:

  1. A program for indexing a sequence file to speed up the binding site search.
  2. A program for retrieving the binding sites of a query sequence.
  3. A program for identifying sites where PCR primers could co-operate to exponentially amplify a sequence
  4. A program for analyzing a set of binding sites to tailor the search for different reaction conditions.
There are also some utilites referenced at the end of this overview. This software is implemented in C. Follow this link to download. .

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 query

Most 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:
Hyfi wraps a number of auxiliary programs, documented here.

PCR primer analysis

The 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 hyfi-cooperative-search:

Analyzing a set of binding sites to customize the search for different reaction conditions

Because 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 utilities

Hyfi has a set of utilities as well. SourceForge.net Logo