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Search · four archives
15 papers · ranked by Valyu relevance
Charlotte Tumescheit, Andrew E. Firth, Katherine Brown, Burkhard Morgenstern
'Burkhard Morgenstern'] Background 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 can lead…
Jiannan Chao, Furong Tang, Lei Xu, Lukasz Kurgan
The continuous development of sequencing technologies has enabled researchers to obtain large amounts of biological sequence data, and this has resulted in increasing demands for software that can perform sequence alignment fast and accurately. A number of algorithms and tools for sequence alignment have been designed…
Chenyue Zhang, Qinxin Wang, Yiyang Li, Anqi Teng + 4 more
'Qiqige Wuyun' 'Wei Zheng' 'Le Nguyen Quoc Khanh'] Multiple sequence alignment (MSA) has evolved into a fundamental tool in the biological sciences, playing a pivotal role in predicting molecular structures and functions. With broad applications in protein and nucleic acid modeling, MSAs continue to underpin…
Tong Zhou, Pinglu Zhang, Quan Zou, Wu Han + 1 more
Multiple sequence alignment (MSA) is crucial in bioinformatics for analyzing biological sequence structures, functions, and phylogenetic inferences (, ). Over the last decade, the costs of next-generation sequencing have halved each year, outpacing the reduction in computational costs. This significant progress has led…
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…
Nimrod Serok, Ksenia Polonsky, Haim Ashkenazy, Itay Mayrose + 3 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 (SoP)…
Krishnendu Sinha, Pier Luigi Martelli
Multiple sequence alignment (MSA) is a foundational operation in computational biology, underpinning phylogenetic reconstruction, functional motif discovery, evolutionary rate estimation, and comparative structural analysis (, ). Despite decades of algorithmic development, accurate alignment of divergent protein…
Yixiao Zhai, Zitong Zhang, Zhen Li
The reliability of multiple sequence alignment (MSA) results directly determines the credibility of the conclusions drawn from biological research. However, MSA is inherently an NP-hard problem, making it theoretically impossible to guarantee a globally optimal solution. Consequently, in addition to developing more…
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…
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…
Jörg Winkler, Gianvito Urgese, Elisa Ficarra, Knut Reinert
Background The function of non-coding RNA sequences is largely determined by their spatial conformation, namely the secondary structure of the molecule, formed by Watson-Crick interactions between nucleotides. Hence, modern RNA alignment algorithms routinely take structural information into account. In order to…
Luisa Santus, Jose Espinosa-Carrasco, Leon Rauschning, Júlia Mir-Pedrol + 12 more
'Júlia Mir-Pedrol' 'Igor Trujnara' 'Alessio Vignoli' 'Leila Mansouri' 'Athanasios Baltzis' 'Evan W Floden' 'Paolo Di\xa0Tommaso' 'Edgar Garriga' 'Adam Gudyś' 'Sebastian Deorowicz' 'Cameron Gilchrist' 'Martin Steinegger' 'Cedric Notredame'] Title: Abstract The computational complexity of many key bioinformatics problems…
Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan
An alternative method to accelerate the computation process is to employ multiple threads for parallel calculation of the non-dependent sections of the sequence alignment. This approach is efficient when the benefit of speeding up these threads outweighs the cost of additional overhead. The multithreaded technique can…
Jannik Olbrich, Thomas Büchler, Enno Ohlebusch, Yann Ponty
After the computation of the anchors, we need to fill the gaps between them. (Note that this can trivially be parallelized because the alignments of two gaps are independent of each other.) For small gaps, we can simply use another multiple-sequence aligner [we use FMAlign2 () and MAFFT ()]. However, when there are…
Xinwei Zhao, Eberhard Korsching, Philip Hublitz
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…