Search · four archives
Search · four archives
16 papers · ranked by Valyu relevance
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…
S. Ali Lajevardy, Mehrdad Kargari
Molecular biology advances in the past few decades have contributed to the rapid increase in genome sequencing of various organisms; sequence alignment is usually considered as the first step in understanding the molecular function of a sequence. An optimal alignment adjusts two or more sequences in a way that it could…
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…
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…
Charlotte Tumescheit, Andrew E. Firth, Katherine Brown
Throughout biology, multiple sequence alignments (MSAs) form the basis of much investigation into biological features and relationships. These alignments are at the heart of many bioinformatics analyses. However, sequences in MSAs are often incomplete or very divergent, which leads to poorly aligned regions or large…
Nimrod Serok, Ksenia Polonsky, Haim Ashkenazy, Itay Mayrose + 2 more
Multiple sequence alignment (MSA) inference is a central task in molecular evolution and comparative genomics, and the reliability of downstream analyses, including phylogenetic inference, depends critically on alignment quality. Despite this importance, most widely used MSA methods optimize the sum-of-pairs (SP)…
Luisa Santus, Jose Espinosa-Carrasco, Leon Rauschning, Júlia Mir-Pedrol + 12 more
The computational complexity of many key bioinformatics problems has resulted in numerous alternative heuristic solutions, where no single approach consistently outperforms all others. This creates difficulties for users trying to identify the most suitable tool for their dataset and for developers managing and…
Liang Hong, Siqi Sun, Liangzhen Zheng, Qingxiong Tan + 1 more
Evolutionarily related sequences provide information for the protein structure and function. Multiple sequence alignment, which includes homolog searching from large databases and sequence alignment, is efficient to dig out the information and assist protein structure and function prediction, whose efficiency has been…
Michael Nute, Ehsan Saleh, Tandy Warnow
The estimation of multiple sequence alignments of protein sequences is a basic step in many bioinformatics pipelines, including protein structure prediction, protein family identification, and phylogeny estimation. Statistical co-estimation of alignments and trees under stochastic models of sequence evolution has long…
Dent Earl, Ngan Nguyen, Glenn Hickey, Robert S. Harris + 21 more
Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark datasets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole genome…
Muhammad Ali Nayeem, Md. Shamsuzzoha Bayzid, Atif Hasan Rahman, Rifat Shahriyar + 1 more
Multiple sequence alignment (MSA) is a basic step in many analyses in computational biology, including predicting the structure and function of proteins, orthology prediction and estimating phylogenies. The objective of MSA is to infer the homology among the sequences of chosen species. Commonly, the MSAs are inferred…
Mathilde Carpentier, Jacques Chomilier
Facing the huge increase of information about proteins, classification has reached the level of a compulsory task, essential for assigning a function to a given sequence, by means of comparison to existing data. Multiple sequence alignment programs have been proven to be very useful and they have already been…
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…
Hao Xuan, Hongyang Sun, Xiangtao Liu, Hanyuan Zhang + 2 more
Sequence alignment underpins nearly every facet of modern genomics, from genetic testing and cancer profiling to functional genome annotation. Yet, despite decades of algorithmic innovation, most existing aligners remain narrowly optimized for specific tasks, fragmenting analytical workflows and limiting…
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…
Mariana Flores-Torres, Laura Gómez-Romero, Joshua I. Haase-Hernández, Israel Aguilar-Ordóñez + 3 more
In this work, we evaluated several tools used for the alignment of short sequences and found that most aligners execute reasonably well for identical sequences, whereas a variety of alignment errors emerge for dissimilar ones. Since alignments are essential in computational biology, we developed ExtendAlign, a…