Related papers: AnySeq: A High Performance Sequence Alignment Libr…
Exact similarity search over large collections of data series is a fundamental operation in modern applications, yet existing solutions are often fragmented, specialized, or tailored to specific execution environments. In this paper, we…
Sequence alignment is a fundamental process in computational biology which identifies regions of similarity in biological sequences. With the exponential growth in the volume of data in bioinformatics databases, the time, processing power,…
Motivation: High-throughput sequencing enables expression analysis at the level of individual transcripts. The analysis of transcriptome expression levels and differential expression estimation requires a probabilistic approach to properly…
Multiple sequence alignment is a basic procedure in molecular biology, and it is often treated as being essentially a solved computational problem. However, this is not so, and here I review the evidence for this claim, and outline the…
The ability to design and optimize biological sequences with specific functionalities would unlock enormous value in technology and healthcare. In recent years, machine learning-guided sequence design has progressed this goal significantly,…
Bioinformatics and Computational Biology are two fields that have been exploiting GPUs for more than two decades, being CUDA the most used programming language for them. However, as CUDA is an NVIDIA proprietary language, it implies a…
Motivation: We introduce SneakySnake, a highly parallel and highly accurate pre-alignment filter that remarkably reduces the need for computationally costly sequence alignment. The key idea of SneakySnake is to reduce the approximate string…
Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed…
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…
Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…
We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous…
Transformer, BERT and their variants have achieved great success in natural language processing. Since Transformer models are huge in size, serving these models is a challenge for real industrial applications. In this paper, we propose…
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…
Sequencing by Emergence (SEQE) is a new single-molecule nucleic acid (DNA/RNA) sequencing technology that estimates sequence as an emergent property of the binding and localization of a repertoire of short oligonucleotide probes. SEQE…
Correct performance assessment is crucial for evaluating modern artificial intelligence algorithms in medicine like deep-learning based medical image segmentation models. However, there is no universal metric library in Python for…
Several of the next generation sequencers are limited in their sample preparation process by the need to make an absolute measurement of the number of template molecules in the library to be sequenced. As currently practiced, the practical…
Liesel is a new probabilistic programming framework developed with the aim of supporting research on Bayesian inference based on Markov chain Monte Carlo (MCMC) simulations in general and semi-parametric regression specifications in…
We consider the correction of errors from nucleotide sequences produced by next-generation targeted amplicon sequencing. The next-generation sequencing (NGS) platforms can provide a great deal of sequencing data thanks to their high…
This paper presents the implementation of a quantum sequence alignment (QSA) algorithm on biological data in environments simulating noisy intermediate-scale quantum (NISQ) computers. The approach to quantum bioinformatics adapts the…
Automatically tuning parallel compute kernels allows libraries and frameworks to achieve performance on a wide range of hardware, however these techniques are typically focused on finding optimal kernel parameters for particular input sizes…