Related papers: Multiple Sequence Alignment System for Pyrosequenc…
DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…
Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that…
Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…
We proposed a probabilistic algorithm to solve the Multiple Sequence Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits the representation of the Multiple Alignment between $D$ sequences as a directed polymer in…
Background: Computational analysis of next-generation sequencing data is outpaced by data generation in many cases. In one such case, paired-end reads can be produced from the Illumina sequencing method faster than they can be overlapped by…
In this paper, we propose DeepAlign, a novel approach to multi-perspective process anomaly correction, based on recurrent neural networks and bidirectional beam search. At the core of the DeepAlign algorithm are two recurrent neural…
Text alignment finds application in tasks such as citation recommendation and plagiarism detection. Existing alignment methods operate at a single, predefined level and cannot learn to align texts at, for example, sentence and document…
Analyses of targeted genomic sequencing data from next-generation-sequencing (NGS) technologies typically involves mapping reads to a reference sequence or clustering reads. For a number of species a reference genome is not available so the…
In this paper we address the application of pre-processing techniques to multi-channel time series data with varying lengths, which we refer to as the alignment problem, for downstream machine learning. The misalignment of multi-channel…
Recent advances in reasoning models have demonstrated significant improvements in accuracy by employing detailed and comprehensive reasoning processes. However, generating these lengthy reasoning sequences is computationally expensive and…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
Pyrosequencing is one of the important next-generation sequencing technologies. We derive the distribution of the number of positive signals in pyrograms of this sequencing technology as a function of flow cycle numbers and nucleotide…
Time Series Alignment is a critical task in signal processing with numerous real-world applications. In practice, signals often exhibit temporal shifts and scaling, making classification on raw data prone to errors. This paper introduces a…
Multiple network alignment is the problem of identifying similar and related regions in a given set of networks. While there are a large number of effective techniques for pairwise problems with two networks that scale in terms of edges,…
We explore connections between metagenomic read assignment and the quantification of transcripts from RNA-Seq data. In particular, we show that the recent idea of pseudoalignment introduced in the RNA-Seq context is suitable in the…
A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of set of species…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
In shotgun sequencing, the input string (typically, a long DNA sequence composed of nucleotide bases) is sequenced as multiple overlapping fragments of much shorter lengths (called \textit{reads}). Modelling the shotgun sequencing pipeline…
Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short…