On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching

We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given pattern of length $m$ in $O(\frac{m}{p}+ \lg p + \lg\lg p\cdot\lg\lg n)$ time for $p \le m$. For approximate pattern matching with $k$ differences or mismatches, we show how to compute all occurrences of a given pattern in $O(\frac{m^k\sigma^k}{p}\max\left(k,\lg\lg n\right)\!+\!(1+\frac{m}{p}) \lg p\cdot \lg\lg n + \text{occ})$ time, where $\sigma$ is the size of the alphabet and $p \le \sigma^k m^k$. The workhorse of our algorithms is a data structure for merging suffix array intervals quickly: Given the suffix array intervals for two patterns $P$ and $P'$, we present a data structure for computing the interval of $PP'$ in $O(\lg\lg n)$ sequential time, or in $O(1+\lg_p\lg n)$ parallel time. All our data structures are of size $O(n)$ bits (in addition to the suffix array)

Desirable properties for XML update mechanisms

The adoption of XML as the default data interchange format and the standardisation of the XPath and XQuery languages has resulted in significant research in the development and implementation of XML databases capable of processing queries efficiently. The ever-increasing deployment of XML in industry and the real-world requirement to support efficient updates to XML documents has more recently prompted research in dynamic XML labelling schemes. In this paper, we provide an overview of the recent research in dynamic XML labelling schemes. Our motivation is to define a set of properties that represent a more holistic dynamic labelling scheme and present our findings through an evaluation matrix for most of the existing schemes that provide update functionality

A basic analysis toolkit for biological sequences

This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for the mentioned string matching and alignment problems. The library consists of C/C++ library functions as well as Perl library functions. It can be interfaced with Bioperl and can also be used as a stand-alone system with a GUI. The software is available at under the GNU GPL

Circular sequence comparison: algorithms and applications

Background: Sequence comparison is a fundamental step in many important tasks in bioinformatics; from phylogenetic reconstruction to the reconstruction of genomes. Traditional algorithms for measuring approximation in sequence comparison are based on the notions of distance or similarity, and are generally computed through sequence alignment techniques. As circular molecular structure is a common phenomenon in nature, a caveat of the adaptation of alignment techniques for circular sequence comparison is that they are computationally expensive, requiring from super-quadratic to cubic time in the length of the sequences. Results: In this paper, we introduce a new distance measure based on q-grams, and show how it can be applied effectively and computed efficiently for circular sequence comparison. Experimental results, using real DNA, RNA, and protein sequences as well as synthetic data, demonstrate orders-of-magnitude superiority of our approach in terms of efficiency, while maintaining an accuracy very competitive to the state of the art

Non-blocking Priority Queue based on Skiplists with Relaxed Semantics

Priority queues are data structures that store information in an orderly fashion. They are of tremendous importance because they are an integral part of many applications, like Dijkstra’s shortest path algorithm, MST algorithms, priority schedulers, and so on. Since priority queues by nature have high contention on the delete_min operation, the design of an efficient priority queue should involve an intelligent choice of the data structure as well as relaxation bounds on the data structure. Lock-free data structures provide higher scalability as well as progress guarantee than a lock-based data structure. That is another factor to be considered in the priority queue design. We present a relaxed non-blocking priority queue based on skiplists. We address all the design issues mentioned above in our priority queue. Use of skiplists allows multiple threads to concurrently access different parts of the skiplist quickly, whereas relaxing the priority queue delete_min operation distributes contention over the skiplist instead of just at the front. Furthermore, a non-blocking implementation guarantees that the system will make progress even when some process fails. Our priority queue is internally composed of several priority queues, one for each thread and one shared priority queue common to all threads. Each thread selects the best value from its local priority queue and the shared priority queue and returns the value. In case a thread is unable to delete an item, it tries to spy items from other threads\u27 local priority queues. We experimentally and theoretically show the correctness of our data structure. We also compare the performance of our data structure with other variations like priority queues based on coarse-grained skiplists for both relaxed and non-relaxed semantics

MergedTrie: Efficient textual indexing

The accessing and processing of textual information (i.e. the storing and querying of a set of strings) is especially important for many current applications (e.g. information retrieval and social networks), especially when working in the fields of Big Data or IoT, which require the handling of very large string dictionaries. Typical data structures for textual indexing are Hash Tables and some variants of Tries such as the Double Trie (DT). In this paper, we propose an extension of the DT that we have called MergedTrie. It improves the DT compression by merging both Tries into a single and by segmenting the indexed term into two fixed length parts in order to balance the new Trie. Thus, a higher overlapping of both prefixes and suffixes is obtained. Moreover, we propose a new implementation of Tries that achieves better compression rates than the Double-Array representation usually chosen for implementing Tries. Our proposal also overcomes the limitation of static implementations that does not allow insertions and updates in their compact representations. Finally, our MergedTrie implementation experimentally improves the efficiency of the Hash Tables, the DTs, the Double-Array, the Crit-bit, the Directed Acyclic Word Graphs (DAWG), and the Acyclic Deterministic Finite Automata (ADFA) data structures, requiring less space than the original text to be indexed.This study has been partially funded by the SEQUOIA-UA (TIN2015-63502-C3-3-R) and the RESCATA (TIN2015-65100-R) projects of the Spanish Ministry of Economy and Competitiveness (MINECO)