HELIOS: High-speed sequence alignment in optics
Fig 2
An example of the proposed coding scheme for DNA, RNA, and protein sequences.
In this example, short DNA, RNA, and protein sequences are coded based on self-label and nearby-label coding schemes with preset values as follows: Offsetself = 450, Stepself = 10, Offsetnearby = 0, Stepnearby = 9, k = 2, and R = 1. The parameter Chi stands for the character positioned in location i as the current character in the self-label coding, and the kth previous character in the nearby-label coding scheme. The parameter V represents a preset value between 0 to 19 for amino acids in the protein sequence and 0 to 3 for nucleotides in the DNA and the RNA sequences. Every character is coded with two values determined by the self-label and nearby-label coding schemes, as represented in its corresponding white block. For nearby-label coding of those characters positioned at the beginning of the sequence, the nearby-label coding wraps around the sequence and considers the desired nearby character at the end of the sequence.