Four-letter alphabet

Fig. 2. Geometric representation of a sequence space. Shown is the sequence space for a dinucleotide using a four-letter alphabet. Each point represents a sequence. Each double-arrowed line represents a Hamming distance h = 1.

Genetic code The information contained in DNA molecules that scientists describe on the basis of a four-letter alphabet (A, C, G, and T). 

DNA—Strands of DNA, or deoxyribonucleic acid, are like long sentences of words composed of a four letter alphabet of nucleotide base pairs A (adenine) T (thymine) C (guanine) and C (cyto-... 

Real chromosomes, of course, come in the four-letter alphabet ACGT. A feature that has not found a use in GAs is the accumulation of junk DNA occurring in eukaryotic chromosomes. About 95% of our DNA resides in these noncoding regions, called introns. Presumably the reason that introns have never disappeared is that there is little selection pressure to get rid of them. However, except for some controversial ideas that introns contain signals for transcription, no positive use for them is known. 

The number of different sequences using a four-letter alphabet (A, C, G, and T or U) increases as 4°, where n is the number of bases in the sequence. The number of different compositions is significantly less, (n-1-4-1) / [n (4 - 1)1] (i.e., the number of combinations of 4 elements chosen n at a time with replacement) [57]. For instance, the number of unique compositions (and hence unique fragment masses) for the complete set of possible 10-mers is 131/(10 x 3 ) or 286, much less than the 4 ° = 1,048,576 unique sequences. Despite this degener-... 

It has been found that three nucleotides select an amino acid for incorporation in the chain we may say that the gene is a sequence of three-letter words (called codons) formed with a four-letter alphabet, A, T, G, C for DNA and the equivalent A, U, G, C for RNA. Thus 146 codons, 438 letters (plus a few to carry the messages to start and to stop... 

DNA strings can be generated from a four-letter alphabet A, C, G, T. A simple sequence model can be developed by assuming that the sequences have been obtained by independent tosses of a four-sided die. Let the data be represented by D and the model by M. The model M has four parameters, namely, P, Pc, Pq/ and Pt for the probabilities of the bases adenine, cyotosine, guanine, and thymine. 

The interaction between base pairs accounts for the ability of DNA to rephcate, as you will learn below. Just as combinations of the 26 letters of the alphabet form words that tell a story in a novel, combinations of the four-letter alphabet of A, T, G, and C form the genes that define our heredity. Each gene is a section of DNA that contains a specific sequence of four bases (A, G, T, and C) and typically contains about 1000 to 2000 base pairs. As of 2004, researchers with the Human Genome Project had discovered that the human body contains about 20 000 to 25 000 genes. 

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