DNA sequence detection by means of two-bit correlation

Abstract

Since the arrival of new devices such as the spatial light modulators based on ferroelectric liquid crystals' , optical pattern recognition has known a revival. Almost all applications in optical pattern recognition are concerned with the recognition of objects in real images with industrial and military applications. For these applications there are major problems to make filters which are able to cope with rotations and scale-changes in the input-image2 along with the presence of noise in the image under investigation. Another recent application is in the field of securing information3. In this article we present a completely new application : we use optical pattern recognition for the recognition of a particular DNA-sequence in a very large DNA-string. We aim to code a genome sequence which is composed of DNAsequences, polymers build up by 4 different organic bases called : Adenine (A), Thymidine (T), Cytosine (C) and Guanine (G). The sequence of these bases in the polymer compose the coding of all biological information necessary to reproduce and grow as a living organism. The human genome is composed of 2.8 billion such bases, a typical virus like HIV contains about 9000 bases. The occurrence of these bases in the large DNA-strings is depending on the kind of DNA but in many cases this occurrence is almost random for the 4 bases. At this moment large efforts are done to resolve the complete sequence of the human genome and a lot of other living organisms. An important topic in genetics is the search for functional sequences in very large DNA-strings to acquire a better understanding of life and diseases. Nowadays, these searches are mainly performed by artificial intelligence techniques4 . In this article we show that optical pattern recognition can be a very effective and very fast alternative for these searches.