A CAM (Content Addressable Memory) Architecture for Codon Matching in DNA Sequences
Parag K. Lala *
Electrical Engineering, Texas A&M University-Texarkana, Texas, USA
*Author to whom correspondence should be addressed.
Abstract
DNA sequences are long strands of four letters – A,T.C and G, that represent the amino-acid building components of proteins . A triplet sequence of adjacent letters on a DNA sequence is known as a codon. Multiple codons represent one of the 20 possible amino acids. DNA sequence matching is used to determine the similarity between an unidentified DNA sequence with the database of other sequences with known characteristics. Those sequences displaying high levels of similarity tend to be similar in nature and thus the matching can be a useful tool in determining the nature of the new genetic sample. This paper presents the conceptual architecture of a content addressable memory that can be used to provide simultaneous comparison of a query DNA sequence with 16 stored sequences, and identifies the ones with the highest number of codon matches with the query sequence.
Keywords: Amino acid, codon, protein, CAM, alignment