14 papers · ranked by Valyu relevance
Panu Horsmalahti
Bucket sort and RADIX sort are two well-known integer sorting algorithms. This paper measures empirically what is the time usage and memory consumption for different kinds of input sequences. The algorithms are compared both from a theoretical standpoint but also on how well they do in six different use cases using…
Samuel King Opoku
—Conventional sorting algorithms make use of such data structures as array, file and list which define access methods of the items to be sorted. These traditional methods – exchange sort, divide and conquer sort, selection sort and insertion sort – require supervisory control program. The supervisory control program…
Rahmani, Mohammad Khalid Imam
Due to the abundance of large number of data repositories with ever-growing volume of online and offline data which are being maintained by enterprise houses, research institutions, medical & healthcare organizations, finding a key is a time-consuming task. For taking a strategic decision, the managers of such…
Stanley P. Y. Fung
Most of us know those simple sorting algorithms like bubble sort very well. Or so we thought – have you ever found yourself needing to write down the pseudocode of bubble sort, only to realise that it is not as straightforward as you think and you couldn't get it right the first time? It needs a bit of care to get the…
Parviz Afereidoon
This paper introduces persiansort, new stable sorting algorithm inspired by Persian rug. Persiansort does not have the weaknesses of mergesort under scenarios involving nearly sorted and partially sorted data, also utilizing less auxiliary memory than mergesort and take advantage of runs. Initial experimental showed…
Juan José Besa, William E. Devanny, David Eppstein, Michael T. Goodrich + 1 more
'Michael T. Goodrich' 'Timothy J. Johnson'] We empirically study sorting in the evolving data model. In this model, a sorting algorithm maintains an approximation to the sorted order of a list of data items while simultaneously, with each comparison made by the algorithm, an adversary randomly swaps the order of…
Jens Oehlschlägel
| Abstract | | 5 | | --- | --- | --- | | Introduction | | 7 | | Sustainability measures | | 8 | | Scope of greeNsort® | | 8 | | Values and principles | | 9 | | Sustainability | | 9 | | Generality | | 9 | | Stability | | 9 | | Robustness | | 9 | | Resilience | | 10 | | Scalability | | 10 | | Reliability | | 10 | |…
Md. Shafiqul Islam, Md. Khaledur Rahman, M. Sohel Rahman
A transposition is an operation that exchanges two adjacent blocks in a permutation. A prefix transposition always moves a prefix of the permutation to another location. In this article, we use a data structure, called the permutation tree, to improve the running time of the best known approximation algorithm (with…
Rahul Varki, Christina Boucher
Relative Lempel–Ziv (RLZ) is an effective compression method for large, repetitive collections; however, the fundamental primitives required to elevate it from a passive archival format to a tractable representation for compressed construction have yet to be fully established. In this paper, we introduce an algorithmic…
Alejandro Gonzales-Irribarren
The General Transfer Format (GTF) is a widely used format for gene annotation data, integral to various downstream analyses. Efficient management and sorting of GTF data are relevant, as unsorted data can intere with computational efficiency and interpretability. Sorted GTF data, on the other hand, enable more…
Md. Khaledur Rahman, M. Sohel Rahman
The genome rearrangement problem computes the minimum number of operations that are required to sort all elements of a permutation. A block-interchange operation exchanges two blocks of a permutation which are not necessarily adjacent and in a prefix block-interchange, one block is always the prefix of that…
Patrick Kunzmann
Alignment searches are fast heuristic methods to identify similar regions between two sequences. This group of algorithms is ubiquitously used in a myriad of software to find homologous sequences or to map sequence reads to genomes. Often the first step in alignment searches is k-mer decomposition: listing all…
Arseny Shur, Ido Tziony, Yaron Orenstein
Minimizers are sampling schemes which are ubiquitous in almost any high-throughput sequencing analysis. Assuming a fixed alphabet of size σ, a minimizer is defined by two positive integers k, w and a linear order ρ on k-mers. A sequence is processed by a sliding window algorithm that chooses in each window of length w…
Ragnar Groot Koerkamp, Igor Martayan
Because of the rapidly-growing amount of sequencing data, computing sketches of large textual datasets has become an essential preprocessing task. These sketches are typically much smaller than the input sequences, but preserve sufficient information for downstream analysis. Minimizers are an especially popular…