helixturnhelix uses the method of Dodd and Egan to find helix-turn-helix nucleic acid binding motifs in proteins.

Here is a sample session with helixturnhelix:

% helixturnhelix
Input sequence: sw:laci_ecoli
Output file [laci_ecoli.hth]:

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

[-outfile] (report)

Output report filename.

Optional qualifiers:

-mean (float)

Mean value.

-sd (float)

Standard Deviation (SD) value.

-minsd (float)

Minimum SD.

-eightyseven (boolean)

Use the old (1987) weight data.