On the Sequence Alignment Problem

One of the central problems of bioinformatics is DNA and protein alignment, which allows one to arrive at the degree of similarity between different DNA and proteins. Graphical bioinformatics [2,3,6] allows one to arrive at measures of similarity-dissimilarity of DNA and proteins without considering DNA or the protein alignment problem. 

There is no doubt that until recently the most that we knew in bioinformatics was due to the availability of very useful computer programs. But that does not mean that further improvements are not possible Very recently, at least a 45-year-old problem of protein sequence alignment, which many believed could not be solved mathematically exactly, has been solved exactly. Exactly means without use of approximations, such as empirical parameters, statistical information, scoring based on penalties for gaps, insertions and deletions, and of course, without use of 

The article in which the exact solution was described was titled Very Efficient Search for Protein Alignment—VESPA [34] because while having an exact solution is important, even more important is that the algorithm leading to the solution is highly efficient. In the next section, we elaborate on the exact solution to the protein alignment problem. 

Let us add that there is an important distinction between computer-based alignment searches and a graphical approach to the same problem. It takes at least two sequences to make computer-based comparisons. In contrast, in the case of graphical representations of DNA and proteins one can characterize a single biological sequence This is a very important distinction between graphical representations of bio-sequences and computer-based analyses of sequences, which one should keep in mind. This allows one to compile, characterize, and catalog DNA and protein sequences of interest for later visitation. 

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