The ordering of the nucleotides in DNA: computational problems in molecular biology

Viewing DNA, RNA and proteins as strings of letters, various algorithms designed for their optimal alignments or their secondary structures have been developed. The results emanating from such sequence editing algorithms are often not correlated with the physio-chemical computations for calculating the detailed atomic coordinates of these molecules. These two aspects are often viewed as separate research entities. Here I attempt to relate various computational aspects of modern molecular biology. In particular, I attempt putting these (along with complementary experimental data) in the framework of a very basic biological question--what fixes the order of the bases in the DNA.