The small nucleolar RNAs (snoRNAs) represent an abundant group of small non-coding RNAs (ncRNAs) in eukaryotes. With the exception of RNase MRP, all the snoRNAs fall into two major families, box C/D and box H/ACA snoRNAs, on the basis of common sequence motifs and structural features. They can be divided into guide and orphan snoRNAs according to the presence or absence of antisense sequence to rRNAs or snRNAs. Recently, thousands of novel snoRNAs were identified from small RNA sequencing datasets in human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana using snoSeekerNGS program.
snoSeeker includes two snoRNA-searching programs, CDseeker and ACAseeker, specific to the detection of C/D snoRNAs and H/ACA snoRNAs from four human–mammal whole-genome alignment (WGA) sequences. Recently, snoSeeker has been used to scan human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana sequences and identified thousuands of snoRNA genes from small RNA deep-sequencing (next generation sequencing) data.