Auxiliary programs

Hyfi is a wrapper that calls sub-modules that implement various parts of the binding partner search. Here is a command line illustrating the computations that hyfi performs when searching for binding sites in chromosome 22, with a stability of at least -7.0 kilocalories per mole:

hyfi-sieve query.fasta | hyfi-lookup - chr22.idx | hyfi-fetch - chr22.fa | hyfi-filter -

| hyfi-distill - The results of the above sequence of commands will be a list of binding sites in chromosome 22 for the query sequence in query.fasta. 

Here is documentation on the programs for binding site search.