In this paper, we propose four index structures for music data retrieval. Based on suffix trees, we develop two index structures called Combined Suffix Tree and Independent Suffix Trees. These methods still show shortcomings for some search functions. Hence we develop another index, called Twin Suffix Trees, to overcome these problems. However, the Twin Suffix Trees lack of scalability when the...

We prove several combinatorial properties of suffix arrays, including a characterization of suffix arrays through a bijection with a certain well-defined class of permutations. Our approach is based on the characterization of Burrows-Wheeler arrays given in [1], that we apply by reducing suffix sorting to cyclic shift sorting through the use of an additional sentinel symbol. We show that the ch...

In recent years the volume of string data has increased exponentially, and the speed at which these data is being generated has also increased. Some examples of string data includes biological sequences, internet webpages, and digitalized documents, to name a few. The indexing of biological sequence data is especially challenging due to the lack of natural word and sentence boundaries. Although...

The book Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology [1] contains about 125 pages devoted to suffix trees, suffix arrays, and their applications in computational biology. A related data structure, the DAWG is discussed via exercises. The book contains a wide range of applications of suffix trees, and while most have a biological “motivation”, at the ti...

Single-nucleotide polymorphisms (SNPs) account for most variations between human genomes. We show how, if the genomes in a database differ only by a reasonable number of SNPs and the substrings between those SNPs are unique, then we can store a fast compressed suffix array for that database.

The suffix array data structure that we present is due to Grossi and Vitter [1]. It uses a recursive construction that inflates the alphabet size, much like the the suffix array construction that we saw in Lecture 18. Building on this, we will construct a low-space suffix tree by augmenting this suffix array with an additional tree structure. This construction is due to Munro, Raman and Rao [2]...

In present time weighted suffix tree is consider as a one of the most important existing data structure used for analyzing molecular weighted sequence. Although a static partitioning based parallel algorithm existed for the construction of weighted suffix tree, but for very long weighted DNA sequences it takes significant amount of time. However, in our implementation of dynamic partition based...

Lowest common ancestor algorithms are in [12, 19, 2]. Algorithms to construct suffix trees in linear time are in [22, 18, 21, 5]. Suffix arrays were introduced in [17]. The linear time construction algorithm for suffix arrays is from [14]. The simple construction of the LCP array from the suffix array is from [15]. The k-mismatch problem is discussed in [7, 16, 1]. The FM index is from [6]. Som...

The suffix tree is one of the most important data structures in string processing and comparative genomics. However, the space consumption of the suffix tree is a bottleneck in large scale applications such as genome analysis. In this article, we will overcome this obstacle. We will show how every algorithm that uses a suffix tree as data structure can systematically be replaced with an algorit...