Procedure and searching results. (a) Procedure for identifying genes that are expressed in ciliated neurons in C. elegans. Known X-boxes used in this procedure are listed in Additional data file 1. The program hmmb was used to build an HMM profile, which was then used to search the promoter sequences using the program hmmfs. (b) The Generic Genome Browser and Bio::DB::GFF database  were used for finding candidate X-boxes and X-box regulated genes.