Prospects and limitations of full-text index structures in genome analysis

The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared

Compressed multiple pattern matching

Peer reviewe

Optimized Indexes for Data Structured Retrieval

The aim of this work is to show the novel index structure based suffix array and ternary search tree with rank and select succinct data structure. Suffix arrays were originally developed to reduce memory consumption compared to a suffix tree and ternary search tree combine the time efficiency of digital tries with the space efficiency of binary search trees. Rank of a symbol at a given position equals the number of times the symbol appears in the corresponding prefix of the sequence. Select is the inverse, retrieving the positions of the symbol occurrences. These operations are widely used in information retrieval and management, being the base of several data structures and algorithms for text collections, graphs, trees, etc. The resulting structure is faster than hashing for many typical search problems, and supports a broader range of useful problems and operations. There for we implement a path index based on those data structures that shown to be highly efficient when dealing with digital collection consist in structured documents. We describe how the index architecture works and we compare the searching algorithms with others, and finally experiments show the outperforms with earlier approaches