A program to identify Helitron given genomic sequences. HelSearch searches for CTRRT in genomic sequence first. To narrow the results, insertion site T was included in this search. The proposed Helitron end (helend) structure is composed of a minimum of 6 hairpin pairs (2 mismatches allowed) upstream of the CTRR, a 2- to 4-bp loop, and 5–8 bp between the hairpin and CTRR. The program was developed in PERL to search for these features in a given genome.