In the previous examples, sequences of whole proteins are sorted into groups of unique permutations. Most often scientists are interested only in certain regions of protein molecules. For example in viral coat proteins changes in the receptor binding domain and the fusion core regions are more important. Therefore, for sorting these segments of the protein molecule it is necessary to carefully cut and paste them into the program, which exercise is generally labor intensive. However, in ChameleonSort there is a provision to load the whole protein sequence and then provide information on the regions of interest for sorting. To achieve this goal, first few letters of specific region of the molecule and the length of the segment of interest are specified in the lower rows of the UI. Up to three regions can be specified in a molecule. This procedure is illustrated in Figure . After filling out the lower two rows of textboxes, whole query protein sequences, taken from databases are entered one at a time into the textbox in the third row as before, followed by clicking on the "Enter" button (after each entry). In this type of query the sorted groups are not in any particular order. Therefore, the groups need to be rearranged after physically inspecting them. To perform this part of the work, first save the session as a windows document. Then retrieve the data into a word processor like Microsoft's word or WordPad. The outcome of sorting of five anonymous sequences of a protein for three different segments is shown in Table . The randomly spread groups from the output are manually arranged in an