13 papers · ranked by Valyu relevance
Chirag Jain, Alexander Dilthey, Sanchit Misra, Haowen Zhang + 1 more
Aligning DNA sequences to an annotated reference is a key step for genotyping in biology. Recent scientific studies have demonstrated improved inference by aligning reads to a variation graph, i.e., a reference sequence augmented with known genetic variations. Given a variation graph in the form of a directed acyclic…
Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan
The rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman-Wunsch method introduces the foundational dynamic programming (DP) matrix calculation for global alignment, which evaluates the overall alignment of sequences. However, this method…
Haojing Shao, Jue Ruan
Increasing the accuracy of the nucleotide sequence alignment is an essential issue in genomics research. Although classic dynamic-programming algorithms (e.g., Smith-Waterman and Needleman–Wunsch) guarantee to produce the optimal result, their time complexity hinders the application of large-scale sequence alignment.…
Sajia Akhter, Robert A Edwards
Next generation sequencing (NGS) technology produces massive amounts of data in a reasonable time and low cost. Analyzing and annotating these data requires sequence alignments to compare them with genes, proteins and genomes in different databases. Sequence alignment is the first step in metagenomics analysis, and…
Daniel Liu, Martin Steinegger
The Smith-Waterman-Gotoh alignment algorithm is the most popular method for comparing biological sequences. Recently, Single Instruction Multiple Data methods have been used to speed up alignment. However, these algorithms have limitations like being optimized for specific scoring schemes, cannot handle large gaps, or…
Pesho Ivanov, Benjamin Bichsel, Martin Vechev
We present a novel A^⋆^ seed heuristic that enables fast and optimal sequence-to-graph alignment, guaranteed to minimize the edit distance of the alignment assuming non-negative edit costs. We phrase optimal alignment as a shortest path problem and solve it by instantiating the A^⋆^ algorithm with our seed heuristic.…
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…
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…
Jordan M. Eizenga, Benedict Paten
Modern genomic sequencing data is trending toward longer sequences with higher accuracy. Many analyses using these data will center on alignments, but classical exact alignment algorithms are infeasible for long sequences. The recently proposed WFA algorithm demonstrated how to perform exact alignment for long, similar…
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…
Daniel J. van Zyl, Marcel Dunaiski, Houriiyah Tegally, Cheryl Baxter + 2 more
The rapid increase in nucleotide sequence data generated by next-generation sequencing (NGS) technologies demands efficient computational tools for sequence comparison. Alignment-based methods, such as BLAST, are increasingly overwhelmed by the scale of contemporary datasets due to their high computational demands for…
Andreas Grigorjew, Artur Gynter, Fernando Dias, Benjamin Buchfink + 2 more
Sequence alignments have become the foundation of life science research by unlocking biological mechanisms through protein comparisons. Despite its methodological success, most algorithmic innovation in the past decades focused on the optimal alignment problem, while often ignoring information derived from suboptimal…