14 papers · ranked by Valyu relevance
Maren Brand, Nguyen Khoa Tran, Philipp Spohr, Sven Schrinner + 1 more
We consider the homo-edit distance problem, which is the minimum number of homo-deletions or homo-insertions to convert one string into another. A homo-insertion is the insertion of a string of equal characters into another string, while a homo-deletion is the inverse operation. We show how to compute the homo-edit…
Hajime Suzuki, Masahiro Kasahara
Pairwise alignment of nucleotide sequences has previously been carried out using the seed- and-extend strategy, where we enumerate seeds (shared patterns) between sequences and then extend the seeds by Smith-Waterman-like semi-global dynamic programming to obtain full pairwise alignments. With the advent of massively…
Nikolai Baudis, Pierre Barbera, Sebastian Graf, Sarah Lutteropp + 3 more
In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available two independent and highly optimized open-source implementations for the pair-wise statistical alignment model, also known as TKF91, that was developed by…
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…
Jonathan Ferrer-Mestres, Thomas G. Dietterich, Olivier Buffet, Iadine Chadès
In conservation of biodiversity, natural resource management and behavioural ecology, stochastic dynamic programming, and its mathematical framework, Markov decision processes (MDPs), are used to inform sequential decision-making under uncertainty. Models and solutions of Markov decision problems should be…
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…
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…
Mikko Rautiainen, Veli Mäkinen, Tobias Marschall
Graphs are commonly used to represent sets of sequences. Either edges or nodes can be labeled by sequences, so that each path in the graph spells a concatenated sequence. Examples include graphs to represent genome assemblies, such as string graphs and de Bruijn graphs, and graphs to represent a pan-genome and hence…
Aditi Jha, Victor Geadah, Jonathan W. Pillow
Understanding complex animal behavior is crucial for linking brain computation to observed actions. While recent research has shifted towards modeling behavior as a dynamic process, few approaches exist for modeling long-term, naturalistic behaviors such as navigation. We introduce discrete Dynamical Inverse…
Enrico Seiler, Myrthe Willemsen, Vitor C. Piro, Knut Reinert
A continued decrease in sequencing costs has facilitated the exponential increase in available sequencing data, with public databases like the European Nucleotide Archive (ENA) and Sequence Read Archive (SRA) reaching well in the order of petabases [1, 2]. This has been the incentive to develop more scalable tools for…
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)…
Jane Kondev, Marc Kirschner, Hernan G. Garcia, Gabriel L. Salmon + 1 more
Many biological processes can be thought of as the result of an underlying dynamics in which the system repeatedly undergoes distinct and abortive trajectories with the dynamical process only ending when some specific process, purpose, structure or function is achieved. A classic example is the way in which…
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…
Boya Wang, Siyuan S. Wang, Cameron Chalk, Andrew D. Ellington + 1 more
DNA is an incredibly dense storage medium for digital data, but computing on the stored information is expensive and slow (rounds of sequencing, in silico computation, and DNA synthesis). Augmenting DNA storage with “in-memory” molecular computation, we use strand displacement reactions to algorithmically modify data…