An efficient approach for sequence matching in large DNA databases

Abstract

In molecular biology, DNA sequence matching is one of the most crucial operations. Since DNA databases contain a huge volume of sequences, fast indexes are essential for efficient processing of DNA sequence matching. In this paper, we first point out the problems of the suffix tree, an index structure widely-used for DNA sequence matching, in respect of storage overhead, search performance, and difficulty in seamless integration with DBMS. Then, we propose a new index structure that resolves such problems. The proposed index structure consists of two parts: the primary part realizes the trie as binary bit-string representation without any pointers, and the secondary part helps fast access to the trie's leaf nodes that need to be accessed for post-processing. We also suggest efficient algorithms based on that index for DNA sequence matching. To verify the superiority of the proposed approach, we conduct performance evaluation via a series of experiments. The results reveal that the proposed approach, which requires smaller storage space, can be a few orders of magnitude faster than the suffix tree.

Approximate pattern matching with gap constraints

“…According to the problem analysis outlined in Subsection 3.2, we know that N(Q1,S,1)=M(Q1,S,0) + M(Q1,S,1). Since the lengths of Q1 and λ are 3 and 4, respectively, there are (λ-1)*m=3*3=9 patterns whose distances to Q1 are 1: Q2=c[0,2]g [1,3] [1,3]t. We know that when d is 0, N(P,S,0) can be solved using PAIG [13].…”

“…These experiments thus verify that an instance in the present study can be transformed into many instances of [13], thereby also verifying the correctness of SONG. [3,9]t [2,5]a [4,9]g [1,8]t [2,9]a P3 g [1,9]t [1,9]a [1,9]g [1,9]t [1,9]a [1,9]g [1,9]t [1,9]a [1,9]g [1,9]t P4 g [1,5]t[0,6]a [2,7]g [3,9]t [2,5]a [4,9]g [1,8]t [2,9]a [1,9]g [1,9] …”

“…ASTRAL95_1_171 is used in [18] and can be downloaded from http://gi.cebitec.uni-bielefeld.de/ comet/force/indexOld.html. Nine patterns (from Q1 to Q9) are g [1,15] Running time (ms) S1 S2 S3 S4 Figure 9. Variation in the running time of SONG with different MinLen.…”

“…These patterns are called Qxy, where x and y are the min gap and max gap, respectively. For instance, Q12 is a [1,2] Table 6 and Figure 6, respectively. From Table 6, we know that N(P,S,d) grows very fast when W increases.…”

“…that threaten our lives and genetic information. Both pattern matching and pattern mining techniques can extract useful information from massive data [1] and pattern matching is a key issue in sequential pattern mining [2]. Pattern matching is one of the essential problems in computer science with broad applications, such as bug detection [3], ontology matching [4], etc.…”