Improving the Sequence Alignment Method by Quantum Multi-Pattern Recognition

A dot matrix approach for sequence alignment is combined with a known quantum multi-pattern recognition method in order to improve the problem of sequence alignment. This dot matrix technique allows the application of some quantum computing principles on the pattern recognition problems like those used in the Grover's algorithm. When the recognized patterns exceed the limit of the 1/3 of the overall patterns, the multi-pattern recognition is accomplished simultaneously with the probability of 100%. The contribution concerns the way that the adopted quantum pattern recognition algorithm is applied speeding up the sequence alignment process. An example application demonstrates the effectiveness of the proposed method. String alignments isn't an essential task only in bioinformatics, but also in calculating the edit distance cost between strings in a natural language or in financial data.