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zoomITS subdivides two types of structures (stem and loop) in ITS2 database into various secondary structures (hairpin loop, bulge, symmetric internal loop, asymmetric internal loop, transition loop, and stem), which enables researchers to interpret sequences with higher resolution. It also converts sequence and structure information into 81 symbols. The program provides a flexible means to identify hCBC/ CBC (Compensatory Base Change) in taxonomic groups whose secondary structures are difficult to predict. Additionally, the program identifies species specific nucleotide (SSN) along with information of various secondary structure, helix indication (I-IV), and pairing mutation in stem structure.

Abstract
Background: Nuclear ribosomal internal transcribed spacer (ITS) region is one of the most widely used for molecular markers in plant and fungi. Although a number of recent studies reported the intra-genomic variations of ITS sequence, a new approach- compensatory base change (CBC) of ITS2 sequence has gained popularity for species delimitation. However, species identification based on CBC requires accurate secondary structure prediction, which presents challenges for taxonomic groups whose secondary structures are difficult to predict.
Results:In addition to the general usages of the program (such as conversion to 81 symbols and subdivision of two categories of secondary structures into 6 categories), zoomITS provides a flexible means to study (h)CBCs even for difficult taxa whose stem alignments are not perfectly identical. It provides lists of potential (h)CBCs within species as well as species unique (h)CBCs, which enables researchers to assess the intra and inter variations of the CBCs and SSNs within species as well as among species. The program provides a useful means to study ITS and has a wide range of applications