Electronic polymerase chain reaction (EPCR) search algorithm

We developed an integer-encoding scheme and a search algorithm for in silico PCR (polymerase chain reaction) amplification that identifies sequence homology with the specified primers and enzymes. Unlike the traditional character-based approach, the EPCR algorithm developed represents DNA sequences as four integer variables. The bit streams in each integer variable reflect the occurrences of nucleotides (A, T C, G) in the sequence. This approach exploits the fact that there are only four possible nucleotides in either DNA or RNA. A sequence of 32 nucleotides therefore can be reduced to four integers. In addition, since nucleotides are individually represented by four integer variables, ambiguities in the sequence (e.g., "N") can be fully resolved and encoded within the four integers.