Search · four archives
Search · four archives
26 papers · ranked by Valyu relevance
Timo Lassmann, Erik LL Sonnhammer
Background The alignment of multiple protein sequences is a fundamental step in the analysis of biological data. It has traditionally been applied to analyzing protein families for conserved motifs, phylogeny, structural properties, and to improve sensitivity in homology searching. The availability of complete genome…
Álvaro Rubio-Largo, Miguel A. Vega-Rodríguez
The alignment among three or more nucleotides/amino-acids sequences at the same time is known as Multiple Sequence Alignment (MSA), an NP-hard optimization problem. The time complexity of finding an optimal alignment raises exponentially when the number of sequences to align increases. In this work, we deal with a…
Claire D. McWhite, Mona Singh
Multiple sequence alignment is a critical step in the study of protein sequence and function. Typically, multiple sequence alignment algorithms progressively align pairs of sequences and combine these alignments with the aid of a guide tree. These alignment algorithms use scoring systems based on substitution matrices…
Yanming Wei, Zhaoyang Huang, Pinglu Zhang, Yizheng Wang + 3 more
Multiple sequence alignment (MSA) is a fundamental problem in bioinformatics. The quality of sequence alignment significantly impacts biological sequence analysis, especially that in next-generation sequencing . MSA results are widely used in various applications, including de novo genome assembly , detection of…
Petar Arsic, Christoph Mayer
We report a convolutional transformer neural network that is capable of aligning multiple nucleotide sequences. The neural network is based on the U-Net commonly used in image segmentation which we employ to transform unaligned sequences to aligned sequences. For alignment scenarios our Ali-U-Net neural network has…
Manish Kumar
One of the most fundamental operations in biological sequence analysis is multiple sequence alignment (MSA). The basic of multiple sequence alignment problems is to determine the most biologically plausible alignments of protein or DNA sequences. In this paper, an alignment method using genetic algorithm for multiple…
Ana Arribas‐Gil, Catherine Matias
We propose an approach for multiple sequence alignment (MSA) derived from the dynamic time warping viewpoint and recent techniques of curve synchronization developed in the context of functional data analysis. Starting from pairwise alignments of all the sequences (viewed as paths in a certain space), we construct a…
Emily G. Light, Morgan E. Prior, Noah M. Daniels, Najib Ishaq
Motivation: The multiple sequence alignment (MSA) problem has been extensively studied, with numerous approaches developed over recent years. With the rapid growth of sequence data, there is an increasing need for fast and accurate MSA tools that scale effectively to large datasets. Building on our previous work on…
David J Russell, Hasan H Otu, Khalid Sayood
Background We propose a multiple sequence alignment (MSA) algorithm and compare the alignment-quality and execution-time of the proposed algorithm with that of existing algorithms. The proposed progressive alignment algorithm uses a grammar-based distance metric to determine the order in which biological sequences are…
Jean-Guy Schneider, Peter Mandile, Steve Versteeg
—Assuring quality of contemporary software systems is a very challenging task due to the often large complexity of the deployment environments in which they will operate. Service virtualization is an approach to this challenge where services within the deployment environment are emulated by synthesising service…
Bryce Kille, Advait Balaji, Fritz J. Sedlazeck, Michael Nute + 1 more
'Todd J. Treangen'] With the arrival of telomere-to-telomere (T2T) assemblies of the human genome comes the computational challenge of efficiently and accurately constructing multiple genome alignments at an unprecedented scale. By identifying nucleotides across genomes which share a common ancestor, multiple genome…
Dent Earl, Ngan Nguyen, Glenn Hickey, Robert S. Harris + 22 more
'Stephen Fitzgerald' 'Kathryn Beal' 'Igor Seledtsov' 'Vladimir Molodtsov' 'Brian J. Raney' 'Hiram Clawson' 'Jaebum Kim' 'Carsten Kemena' 'Jia-Ming Chang' 'Ionas Erb' 'Alexander Poliakov' 'Minmei Hou' 'Javier Herrero' 'William James Kent' 'Victor Solovyev' 'Aaron E. Darling' 'Jian Ma' 'Cedric Notredame' 'Michael Brudno'…
Saikat Chakrabarti, Nitin Bhardwaj, Prem A Anand, Ramanathan Sowdhamini
'Ramanathan Sowdhamini'] Background Multiple sequence alignment algorithms are very important tools in molecular biology today. Accurate alignment of proteins is central to several areas such as homology modelling, docking studies, understanding evolutionary trends and study of structure-function relationships. In…
Ravi Kumar Yadav Dega, Gunes Ercal
Multiple sequence alignment is increasingly important to bioinformatics, with several applications ranging from phylogenetic analyses to domain identification. There are several ways to perform multiple sequence alignment, an important way of which is the progressive alignment approach studied in this work. Progressive…
Kristóf Takács
| 1. Introduction | | 1 | | --- | --- | --- | | 2. Definitions and notations | | 3 | | 3. Multiple sequence alignment for length-1 sequences | | 5 | | 3.1. | Multiple sequence alignment for length-1 sequences using unit | | | metric | | 5 | | 3.2. Multiple sequence alignment for length-1 sequences using arbit | | | |…
Dimitrii O. Kostenko, Eugene V. Korotkov, Cristoforo Comi, Benoit Gauthier + 2 more
'Benoit Gauthier' 'Dimitrios H. Roukos' 'Alfredo Fusco'] The aim of this work was to compare the multiple alignment methods MAHDS, T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK in their ability to align highly divergent amino acid sequences. To accomplish this, we created test amino acid sequences with an…
David A. Morrison
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 requirements for a solution. The goal of alignment is often stated to be to…
Suchindra, P. Nagaraj
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 sequencing algorithms developed over the past decades but the sequence alignment using…
Qikai Yang, Tandy Warnow
PASTA is a method for estimating alignments and trees that has been able to provide excellent accuracy on large sequence datasets. By design, PASTA operates using iteration, in which the tree from the previous iteration is used to inform a divide-and-conquer strategy during which a new alignment is computed on the…
Xinwei Zhao, Eberhard Korsching
DNA and RNA nucleotide sequences are ubiquitous in all biological cells, serving as both a comprehensive library of capabilities for the cells and as an impressive regulatory system to control cellular function. The multi-alignment framework (MAF) provided in this study offers a user-friendly platform for sequence…
Authors not listed
The Protein Data Bank (PDB) is one of the richest open‑source repositories in biology, housing over 277,000 macromolecular structural models alongside much of the experimental data that underpins these models. By systematically collecting, validating, and indexing these models, the PDB has accelerated structural…
Authors not listed
Proteochemometric models (PCM) are used in computational drug discovery to leverage both protein and ligand representations for bioactivity prediction. While machine learning (ML) and deep learning (DL) have come to dominate PCMs, often serving as scoring functions, rigorous evaluation standards have not always been…
Joseph Redshaw, Darren Ting, Alex Brown, Jonathan Hirst + 1 more
Antimicrobial peptides (AMPs) represent a potential solution to the growing problem of antimicrobial resistance, yet their identification through wet-lab experiments is a costly and timeconsuming process. Accurate computational predictions would allow rapid in silico screening of candidate AMPs, thereby accelerating…
Lim Heo, Collin Arbour, Michael Feig
Protein structures provide valuable information for understanding biological processes. Protein structures can be determined by experimental methods such as X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, or cryogenic electron microscopy. As an alternative, in silico methods can be used to predict…
Babu Bassa
In this communication the author describes a software tool named "ChameleonSort". The software program, developed by the present author is useful in the sorting of biological sequence variants like those accumulating mutations while diverging from the common ancestors. Examples include viral protein variants, protein…
Jérôme Eberhardt, Markus Lill, Torsten Schwede
This study introduces a novel Bayesian Optimization (BO) method to support the design and optimization of bioactive peptide sequences in the context of a fully automated closed-loop Design-Make-Test (DMT) pipeline. Using the major histocompatibility complex class I receptor system as test case, we showed that BO is…