15 papers · ranked by Valyu relevance
Quim Aguado-Puig, Max Doblas, Christos Matzoros, Antonio Espinosa + 3 more
Advances in genomics and sequencing technologies demand faster and more scalable analysis methods that can process longer sequences with higher accuracy. However, classical pairwise alignment methods, based on dynamic programming (DP), impose impractical computational requirements to align long and noisy sequences like…
Felix Kallenborn, Fawaz Dabbaghie, Martin Steinegger, Bertil Schmidt
The continually increasing volume of sequence data results in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments based on dynamic programming is an important part in many bioinformatics pipelines and a major contributor to overall runtime due to the associated quadratic…
Tazin Rahman, Oieswarya Bhowmik, Ananth Kalyanaraman
Long read technologies are continuing to evolve at a rapid pace, with the latest of the high fidelity technologies delivering reads over 10Kbp with high accuracy (99.9%). Classical long read assemblers produce assemblies directly from long reads. Hybrid assembly workflows provide a way to combine partially constructed…
Guohao Dou
We propose an algorithm to simulate Markovian SIS epidemics with homogeneous rates and pairwise interactions on a fixed undirected graph, assuming a distributed memory model of parallel programming and limited bandwidth. We offer an implementation of the algorithm in the form of pseudocode in the Appendix. Also, we…
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…
Wilfried Agbeto, Camille Coti, Vladimir Reinharz
Advances in graph algorithmics have allowed in-depth study of many natural objects from molecular biology or chemistry to social networks. Particularly in molecular biology and cheminformatics, understanding complex structures by identifying conserved sub-structures is a key milestone towards the artificial design of…
Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
Durbin’s positional Burrows-Wheeler transform (PBWT) enables algorithms with the optimal time complexity of O(MN) for reporting all vs all haplotype matches in a population panel with M haplotypes and N variant sites. However, even this efficiency may still be too slow when the number of haplotypes reaches millions. To…
Lorién López-Villellas, Cristian Iñiguez, Albert Jiménez-Blanco, Quim Aguado-Puig + 4 more
Advances in DNA sequencing have outpaced advances in computation, making sequence alignment a major bottleneck in genome data analyses. Classical dynamic programming (DP) algorithms are particularly memory-intensive, especially when computing gap-affine and dual gap-affine alignments. Existing strategies to reduce…
Sumesh Kumar, Joseph Zambreno, Ashfaq Khokhar, Shoaib Akram + 1 more
Improving the speed and efficiency of database search algorithms that deduce peptides from mass spectrometry (MS) data has been an active area of research for more than three decades. The significance of the need for faster database search methods has rapidly increased due to the growing interest in studying non-model…
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…
Ragnar Groot Koerkamp
We introduce APA2, an exact global pairwise aligner with respect to edit distance. The goal of APA2 is to unify the near-linear runtime of APA on similar sequences with the efficiency of dynamic programming (DP) based methods. Like Edlib, APA2 uses Ukkonen’s band doubling in combination with Myers’ bitpacking. APA2 1)…
Bertil Schmidt, Felix Kallenborn, Alejandro Chacon, Christian Hundt
The maximal sensitivity for local pairwise alignment makes the Smith-Waterman algorithm a popular choice for protein sequence database search. However, its quadratic time complexity makes it compute-intensive. Unfortunately, current state-of-the-art software tools are not able to leverage the massively parallel…
Max Doblas, Oscar Lostes-Cazorla, Quim Aguado-Puig, Cristian Iñiguez + 2 more
Pairwise sequence alignment is a core component of multiple sequencing-data analysis tools. Recent advancements in sequencing technologies have enabled the generation of longer sequences at a much lower price. Thus, long-read sequencing technologies have become increasingly popular in sequencing-based studies. However…
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.…
Yuru Song, Marcus K. Benna
Cortical neurons often establish multiple synaptic contacts with the same postsynaptic neuron. To avoid functional redundancy of these parallel synapses, it is crucial that each synapse exhibits distinct computational properties. Here we model the current to the soma contributed by each synapse as a sigmoidal…