Quantum search algorithms are considered in the context of protein sequence comparison in bioinformatics. Given a sample protein sequence of length m (i.e., m residues), the problem considered is to find an optimal match in a large database containing N residues. Initially, Grover's quantum search algorithm is applied to a simple illustrative case-namely, where the database forms a complete set of states over the 2(m) basis states of a m qubit register, and thus is known to contain the exact sequence of interest. This example demonstrates explicitly the typical O(square root of [N]) speedup on the classical O(N) requirements. An algorithm is then presented for the (more realistic) case where the database may contain repeat sequences, and may not necessarily contain an exact match to the sample sequence. In terms of minimizing the Hamming distance between the sample sequence and the database subsequences the algorithm finds an optimal alignment, in O(square root of [N]) steps, by employing an extension of Grover's algorithm, due to Boyer et al. for the case when the number of matches is not a priori known.
Quantum search algorithms are considered in the context of protein sequence comparison in bioinformatics. Given a sample protein sequence of length m (i.e., m residues), the problem considered is to find an optimal match in a large database containing N residues. Initially, Grover's quantum search algorithm is applied to a simple illustrative case-namely, where the database forms a complete set of states over the 2(m) basis states of a m qubit register, and thus is known to contain the exact sequence of interest. This example demonstrates explicitly the typical O(square root of [N]) speedup on the classical O(N) requirements. An algorithm is then presented for the (more realistic) case where the database may contain repeat sequences, and may not necessarily contain an exact match to the sample sequence. In terms of minimizing the Hamming distance between the sample sequence and the database subsequences the algorithm finds an optimal alignment, in O(square root of [N]) steps, by employing an extension of Grover's algorithm, due to Boyer et al. for the case when the number of matches is not a priori known.
Grover's quantum algorithm was developed to solve the problem of searching an unstructured database for a certain unique element. In general, this problem can be formulated as follows: an unstructured database consists of elements and contains one unique element that has a certain property that can be tested with polynomial complexity, and which must be found with minimal time and complexity. Classical methods require querying the database to find the desired element, while Grover's algorithm allows you to perform only approximately steps, which are iterations of the procedure, to the database and be sure that the resulting element will be exactly the desired element with a probability close to 1. As in quantum algorithms aimed at cryptanalysis of symmetric transformations, Grover's algorithm repeats the procedure (Grover's iteration) to increase the probability of obtaining the correct result. Similarly to such algorithms in Grover's method, when iterations are continued after reaching the required number of iterations, the probability of obtaining the correct result decreases. This is due to the fact that during the execution of Grover's iteration, a rotation is performed in the complex space. Thus, each iteration, making a turn, brings the register closer and closer to the desired state, but at a certain point a maximum closeness is reached, at which the continued use of iterations will lead to a turn past the desired state, which will move the state of the system away from the desired state. The database for this algorithm can be any search space consisting of a certain number of elements. So, for example, it can be applied to find a secret key for a symmetric cryptograms formation or to find a collision for a hashing function.
Many classes of algorithms that suffer from large complexities when implemented on conventional computers may be reformulated resulting in greatly reduced complexity when implemented on quantum computers. The dramatic reductions in complexity for certain types of quantum algorithms coupled with the computationally challenging problems in some bioinformatics problems motivates researchers to devise efficient quantum algorithms for sequence (DNA, RNA, protein) analysis. This chapter shows that the important sequence classification problem in bioinformatics is suitable for formulation as a quantum algorithm. This chapter leverages earlier research for sequence classification based on Extensible Markov Model (EMM) and proposes a quantum computing alternative. The authors utilize sequence family profiles built using EMM methodology which is based on using pre-counted word data for each sequence. Then a new method termed quantum seeding is proposed for generating a key based on high frequency words. The key is applied in a quantum search based on Grover algorithm to determine a candidate set of models resulting in a significantly reduced search space. Given Z as a function of M models of size N, the quantum version of the seeding algorithm has a time complexity in the order of as opposed to O(Z) for the standard classic version for large values of Z.
Many classes of algorithms that suffer from large complexities when implemented on conventional computers may be reformulated resulting in greatly reduced complexity when implemented on quantum computers. The dramatic reductions in complexity for certain types of quantum algorithms coupled with the computationally challenging problems in some bioinformatics problems motivates researchers to devise efficient quantum algorithms for sequence (DNA, RNA, protein) analysis. This chapter shows that the important sequence classification problem in bioinformatics is suitable for formulation as a quantum algorithm. This chapter leverages earlier research for sequence classification based on Extensible Markov Model (EMM) and proposes a quantum computing alternative. The authors utilize sequence family profiles built using EMM methodology which is based on using pre-counted word data for each sequence. Then a new method termed quantum seeding is proposed for generating a key based on high frequency words. The key is applied in a quantum search based on Grover algorithm to determine a candidate set of models resulting in a significantly reduced search space. Given Z as a function of M models of size N, the quantum version of the seeding algorithm has a time complexity in the order of as opposed to O(Z) for the standard classic version for large values of Z.
IntroductionFor a search problem associated with a unsorted database, the remarkable Grover's quantum algorithm (1) provides a quadratic speedup over its classical counterpart.The search problem can be described as follows: for a given function f , there exists one unknown element in the set {0, 1, ..., N -1} that satisfies f (x)=-1, say x = τ, whereas the other N -1o n e sg i v e f (x)=1.How many times of evaluations of f are required to determine the element τ for f (τ)=-1?Through a conventional algorithm, one needs O(N) trials to achieve this aim.How about the utility of quantum algorithm for the search?For the scenario in the quantum world, the search problem can be rephrased in the quantum mechanical language: for a given unitary operator I τ , that is sometimes called the oracle operator, and a set of state vectors (orthonormal basis): s = {|0 , |1 , ..., |N -1 }, I τ |x = |x for all states in the set except I τ |x = -|x for x = τ.H owma n yqueriesofI τ are required to determine |τ ?By Grover's algorithm, one needs only O( √ N) quantum mechanical steps to find the marked state |τ out.It has been shown that Grover's algorithm is optimal since it needs minimal oracle calls to perform a quantum search (2).The quantum searching process will be briefly reviewed as follows.The first step of Grover's algorithm is to prepare a superposition state of all elements with uniform probability amplitude:Then apply the Grover kernel G = -I η I τ to |s ,w h er eI η is a unitary operator and contains no bias against the marked state.For large N,a f t e ra b o u tm = π √ N/4 repetitions of G operations, the probability to observe |τ is close to one, i.e., G m |s ∼ |τ .( 2 ) Since every single G involves one query of I τ ,onlyO( √ N) searching steps are required for a quantum search task.In what follows, we will first investigate on the general SU(2) formulation for the kernel of Grover's searching operator G.The discussions of quantum searching certainty, robustness, and the analog analogue version of the Grover's algorithm will be given afterwards.
We investigated the use of the quantum Grover algorithm in the mass-spectrometry-based protein identification process. The approach coded the mass spectra on a quantum register and uses the Grover search algorithm for searching multiple solutions to find matches from a database. Measurement of the fidelity between the input and final states was used to quantify the similarity between the experimental and theoretical spectra. The optimal number of iteration is proven to be pi/4sqrt[N/k] , where k refers to the number of marked states. We found that one iteration is sufficient for the search if we let more that 62% of the N states be marked states. By measuring the fidelity after only one iteration of Grover search, we discovered that it resembles that of the correlation-based measurement used in the existing protein identification software. We concluded that the quantum Grover algorithm can be adapted for a correlation-based mass spectra database search, provided that decoherence can be kept to a minimum.
In computational biology, desired patterns are searched in large text databases, and an exact match is preferable. Classical benchmark algorithms obtain competent solutions for pattern matching in time, whereas quantum algorithm design is based on Grover's method, which completes the search in time. This paper briefly explains existing quantum algorithms and defines their processing limitations. Our initial work overcomes existing algorithmic constraints by proposing the quantum-based combined exact (QBCE) algorithm for the pattern-matching problem to process exact patterns. Next, quantum random access memory (QRAM) processing is discussed, and based on it, we propose the QRAM processing-based exact (QPBE) pattern-matching algorithm. We show that to find all occurrences of a pattern, the best case time complexities of the QBCE and QPBE algorithms are , and the exceptional worst case is bounded by . Thus, the proposed quantum algorithms achieve computational speedup. Our work is proved mathematically and validated with simulation, and complexity analysis demonstrates that our quantum algorithms are better than existing pattern-matching methods.