Search results for " data structure."
showing 10 items of 88 documents
Detecting mutations by eBWT
2018
In this paper we develop a theory describing how the extended Burrows-Wheeler Transform (eBWT) of a collection of DNA fragments tends to cluster together the copies of nucleotides sequenced from a genome G. Our theory accurately predicts how many copies of any nucleotide are expected inside each such cluster, and how an elegant and precise LCP array based procedure can locate these clusters in the eBWT. Our findings are very general and can be applied to a wide range of different problems. In this paper, we consider the case of alignment-free and reference-free SNPs discovery in multiple collections of reads. We note that, in accordance with our theoretical results, SNPs are clustered in th…
The colored longest common prefix array computed via sequential scans
2018
Due to the increased availability of large datasets of biological sequences, the tools for sequence comparison are now relying on efficient alignment-free approaches to a greater extent. Most of the alignment-free approaches require the computation of statistics of the sequences in the dataset. Such computations become impractical in internal memory when very large collections of long sequences are considered. In this paper, we present a new conceptual data structure, the colored longest common prefix array (cLCP), that allows to efficiently tackle several problems with an alignment-free approach. In fact, we show that such a data structure can be computed via sequential scans in semi-exter…
Alignment-free sequence comparison using absent words
2018
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free techniques, which are based on measures referring to the composition of sequences in terms of their constituent patterns. These measures, such as $q$-gram distance, are usually computed in time linear with respect to the length of the sequences. In this paper, we focus on the complementary idea: how two sequences can be efficiently compared based on information that does not occur in the sequences. A word is an {\em absent word} of some sequence if it does not oc…
Block Sorting-Based Transformations on Words: Beyond the Magic BWT
2018
The Burrows-Wheeler Transform (BWT) is a word transformation introduced in 1994 for Data Compression and later results have contributed to make it a fundamental tool for the design of self-indexing compressed data structures. The Alternating Burrows-Wheeler Transform (ABWT) is a more recent transformation, studied in the context of Combinatorics on Words, that works in a similar way, using an alternating lexicographical order instead of the usual one. In this paper we study a more general class of block sorting-based transformations. The transformations in this new class prove to be interesting combinatorial tools that offer new research perspectives. In particular, we show that all the tra…
Effect of raster resolution and polygon-conversion algorithm on landslide susceptibility mapping
2016
The choice of the proper resolution in landslide susceptibility mapping is a worth considering issue. If, on the one hand, a coarse spatial resolution may describe the terrain morphologic properties with low accuracy, on the other hand, at very fine resolutions, some of the DEM-derived morphometric factors may hold an excess of details. Moreover, the landslide inventory maps are represented throughout geospatial vector data structure, therefore a conversion procedure vector-to-raster is required.This work investigates the effects of raster resolution on the susceptibility mapping in conjunction with the use of different algorithms of vector-raster conversion. The Artificial Neural Network t…
Stability-Based Model Selection for High Throughput Genomic Data: An Algorithmic Paradigm
2012
Clustering is one of the most well known activities in scien- tific investigation and the object of research in many disciplines, ranging from Statistics to Computer Science. In this beautiful area, one of the most difficult challenges is the model selection problem, i.e., the identifi- cation of the correct number of clusters in a dataset. In the last decade, a few novel techniques for model selection, representing a sharp departure from previous ones in statistics, have been proposed and gained promi- nence for microarray data analysis. Among those, the stability-based methods are the most robust and best performing in terms of predic- tion, but the slowest in terms of time. Unfortunately…
On-line construction of two-dimensional suffix trees
1997
We present a new technique, which we refer to as implicit updates, based on which we obtain: (a) an algorithm for the on-line construction of the Lsuffix tree of an n x n matrix A — this data structure, described in [13], is the two-dimensional analog of the suffix tree of a string; (b) simple algorithms implementing primitive operations for LZ1-type on-dine lossless image compression methods. Those methods, recently introduced by Storer [35], are generalizations of LZl-type compression methods for strings (see also [24, 31]). For the problem in (a), we get nearly an order of magnitude improvement over algorithms that can be derived from known techniques [13]. For the problem in (b), we do …
Table Compression
2016
Data Compression Techniques for massive tables are described. Related methodological results are also presented.
Fully Automatic Trunk Packing with Free Placements
2010
We present a new algorithm to compute the volume of a trunk according to the SAE J1100 standard. Our new algorithm uses state-of-the-art methods from computational geometry and from combinatorial optimization. It finds better solutions than previous approaches for small trunks.
Persistent software transactional memory in Haskell
2021
Emerging persistent memory in commodity hardware allows byte-granular accesses to persistent state at memory speeds. However, to prevent inconsistent state in persistent memory due to unexpected system failures, different write-semantics are required compared to volatile memory. Transaction-based library solutions for persistent memory facilitate the atomic modification of persistent data in languages where memory is explicitly managed by the programmer, such as C/C++. For languages that provide extended capabilities like automatic memory management, a more native integration into the language is needed to maintain the high level of memory abstraction. It is shown in this paper how persiste…