12 papers · ranked by Valyu relevance
Fabio F. de Oliveira, Leonardo A. Dias, Marcelo A. C. Fernandes
In bioinformatics, alignment is an essential technique for finding similarities between biological sequences. Usually, the alignment is performed with the Smith-Waterman (SW) algorithm, a well-known sequence alignment technique of high-level precision based on dynamic programming. However, given the massive data volume…
Ragnar Groot Koerkamp, Giulio Ermanno Pibiri
Given a string S, a minimizer scheme is an algorithm defined by a triple (k, w, 𝒪) that samples a subset of k-mers (k-long substrings) from a string S. Specifically, it samples the minimal k-mer according to the order 𝒪 from each window of w consecutive k-mers in S. Because consecutive windows can sample the same…
Ragnar Groot Koerkamp, Giulio Ermanno Pibiri
Given a string S, a minimizer scheme is an algorithm defined by a triple (k, w, 𝒪) that samples a subset of k-mers (k-long substrings) from a string S. Specifically, it samples the smallest k-mer according to the order 𝒪 from each window of w consecutive k-mers in S. Because consecutive windows can sample the same…
Martin Šošić, Mile Šikić
We present Edlib, an open-source C/C++ library for exact pairwise sequence alignment using edit distance. We compare Edlib to other libraries and show that it is the fastest while not lacking in functionality, and can also easily handle very large sequences. Being easy to use, flexible, fast and low on memory usage, we…
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…
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…
Changin Oh, Kathleen P. Wilkie
We present the Toroidal Search Algorithm (TSA), a novel population-based metaheuristic optimization method inspired by the topology of a torus. Conventional metaheuristics frequently suffer from boundary stagnation, a phenomenon that severely degrades performance in bounded and high-dimensional search spaces. TSA…
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…
Páll Melsted, Bjarni V. Halldórsson
Several applications in bioinformatics, such as genome assemblers and error corrections methods, rely on counting and keeping track of k-mers (substrings of length k). Histograms of k-mer frequencies can give valuable insight into the underlying distribution and indicate the error rate and genome size sampled in the…
Kazunori D Yamada
In the deep learning era, a gradient descent method is the most common method to optimize parameters of neural networks. Among various mathematical optimization methods, a gradient descent method is the most naive method. Although controlling a learning rate of the method is necessary for quick convergence, the…
Bastian Wiederhold, Martin Stemmler, Andreas V.M. Herz
While our senses transmit information at rates exceeding 10^6^ bit/s, high-level cognitive processing is thought to be much slower, on the order of 10 bit/s regardless of the task^1^. It is unclear, though, whether this limit holds when the human mind is challenged. To test how fast one can process abstract…
Hongyu Zheng, Carl Kingsford, Guillaume Marçais
Minimizers are methods to sample k-mers from a sequence, with the guarantee that similar set of k-mers will be chosen on similar sequences. It is parameterized by the k-mer length k, a window length w and an order on the k-mers. Minimizers are used in a large number of softwares and pipelines to improve computation…