Article
Biochemical Research Methods
Lang Zhou, Tingze Feng, Shuangbin Xu, Fangluan Gao, Tommy T. Lam, Qianwen Wang, Tianzhi Wu, Huina Huang, Li Zhan, Lin Li, Yi Guan, Zehan Dai, Guangchuang Yu
Summary: The identification of conserved and variable regions in multiple sequence alignment is crucial for accelerating gene function understanding. ggmsa, an R package, provides various display methods to mine comprehensive sequence features, supports correlation analysis, and offers a new visualization method for genome alignment, aiding researchers in discovering MSA patterns and making decisions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Biochemical Research Methods
Yongqing Zhang, Qiang Zhang, Jiliu Zhou, Quan Zou
Summary: Multiple sequence alignment (MSA) is an important aspect in bioinformatics, revealing potential information in biological sequences. However, MSA faces new challenges with the increasing sequence scale and demand for alignment accuracy. Developing an efficient and accurate MSA strategy has become a research hotspot in bioinformatics. This work summarizes MSA algorithms and their applications in bioinformatics, providing valuable insights for further research and contributions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Vladimir Smirnov, Tandy Warnow
Summary: MAGUS is a new technique for computing large-scale alignments, similar to PASTA but faster and more accurate. It utilizes a divide-and-conquer approach and merges subset alignments using a Graph Clustering Merger.
Article
Biochemical Research Methods
Maksim Shegay, Vytas K. Svedas, Vladimir V. Voevodin, Dmitry A. Suplatov, Nina N. Popova
Summary: With the increasing availability of 3D data, there is a shift towards content-rich 3D alignments in comparative bioinformatic analysis, leading to the need for new ways to improve 3D superimposition accuracy. The proposed guide tree optimization with genetic algorithm (GA) significantly improves alignment quality for multiple protein 3D structures. Implementation of the GA-based approach in M3DSA algorithms demonstrates statistically significant improvements in TM-score quality indicators on various datasets, showing potential for optimizing 3D alignments across diverse protein superfamilies.
Article
Multidisciplinary Sciences
Yejin Lee, Dong U. Woo, Yang Jae Kang
Summary: Due to the advancement of sequencing technology and decreased cost, numerous whole genome sequences have been obtained, leading to the discovery of extensive genetic variations. The aim of this research was to verify and establish a reliable set of SNPs through different reference genomes and publicly available databases, resulting in the creation of an accessible database.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Juntao Chen, Jiannan Chao, Huan Liu, Fenglong Yang, Quan Zou, Furong Tang
Summary: In this study, a novel method called StarTree is proposed to construct a guide tree quickly, and the FM-index and k-banded dynamic programming algorithm are applied for similar region detection and sequence alignment. Comparing with other methods, the results show that the guide tree constructed by StarTree clustering method is more accurate than PartTree and requires less time and memory than UPGMA and mBed methods. In the alignment of simulated datasets, WMSA 2 demonstrates excellent time and memory efficiency. In the alignment of 1 million SARS-CoV-2 genomes, the win-win mode of WMSA 2 significantly reduces the time consumption.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Niema Moshiri
Summary: ViralMSA is a user-friendly reference-guided MSA tool that allows for the alignment of large viral genome datasets efficiently, but it omits insertions with respect to the reference genome.
Article
Biochemistry & Molecular Biology
Dimitrii O. Kostenko, Eugene Korotkov
Summary: The aim of this study was to compare the performance of multiple alignment methods in aligning highly divergent amino acid sequences. The results showed that although MAHDS had slightly lower quality alignments compared to other algorithms, it compensated with greater statistical significance. Additionally, MAHDS outperformed other methods in constructing statistically significant alignments for highly divergent protein sequences.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Alexis Dereeper, Marilyne Summo, Damien F. Meyer
Summary: PanExplorer is a web application that provides various genomic analyses and reports, aiding in the better understanding of bacterial pan-genomes.
Article
Biochemical Research Methods
Mengmeng Kuang, Yong Zhang, Tak-Wah Lam, Hing-Fung Ting
Summary: In this paper, the authors propose a data-centric approach for Multiple Sequence Alignment (MSA) construction problem. They use classification models trained from existing benchmark data to guide the construction. The authors demonstrate that shallow machine-learning algorithms are sufficient to train sensitive models for the classifications. They implement a new MSA pipeline, MLProbs, which outperforms other popular alignment tools in terms of TC score.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Mathematics
Mohammed Ibrahim, Umi Kalsom Yusof, Taiseer Abdalla Elfadil Eisa, Maged Nasser
Summary: This paper introduces an enhanced evolutionary-based multi-objective optimization method to simplify the problem of multiple sequence alignment and successfully mitigate computational complexities. Through experimental comparison and statistical analysis, the superior solution quality of this method is verified, providing promise for advancing multiple sequence alignment in the field of bioinformatics.
Article
Biotechnology & Applied Microbiology
Glenn Hickey, Jean Monlong, Jana Ebler, Adam M. Novak, Jordan M. Eizenga, Yan Gao, Tobias Marschall, Heng Li, Benedict Paten, Haley J. Abel, Lucinda L. Antonacci-Fulton, Mobin Asri, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Guillaume Bourque, Silvia Buonaiuto, Andrew Carroll, Mark J. P. Chaisson, Pi-Chuan Chang, Xian H. Chang, Haoyu Cheng, Justin Chu, Sarah Cody, Vincenza Colonna, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Daniel Doerr, Peter Ebert, Jana Ebler, Evan E. Eichler, Jordan M. Eizenga, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Xiaowen Feng, Christian Fischer, Paul Flicek, Giulio Formenti, Adam Frankish, Robert S. Fulton, Yan Gao, Shilpa Garg, Erik Garrison, Nanibaa' A. Garrison, Carlos Garcia Giron, Richard E. Green, Cristian Groza, Andrea Guarracino, Leanne Haggerty, Ira M. Hall, William T. Harvey, Marina Haukness, David Haussler, Simon Heumos, Glenn Hickey, Kendra Hoekzema, Thibaut Hourlier, Kerstin Howe, Miten Jain, Erich D. Jarvis, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Wen-Wei Liao, Shuangjia Lu, Tsung-Yu Lu, Julian K. Lucas, Magalhaes Hugo, Marco-Sola Santiago, Pierre Marijon, Charles Markello, Tobias Marschall, Fergal J. Martin, Ann McCartney, Jennifer McDaniel, Karen H. Miga, Matthew W. Mitchell, Jean Monlong, Jacquelyn Mountcastle, Katherine M. Munson, Moses Njagi Mwaniki, Maria Nattestad, Adam M. Novak, Sergey Nurk, Hugh E. Olsen, Nathan D. Olson, Trevor Pesout, Adam M. Phillippy, Alice B. Popejoy, David Porubsky, Pjotr Prins, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen Schultz, Kishwar Shafin, Jonas A. Sibbesen, Jouni Siren, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Francoise Thibaud-Nissen, Chad Tomlinson, Francesca Floriana Tricomi, Flavia Villani, Mitchell R. Vollger, Justin Wagner, Brian Walenz, Ting Wang, Jonathan M. D. Wood, Aleksey Zimin, Justin M. Zook
Summary: Genome assemblies are used to directly construct genome graphs, which can represent various forms of genetic variation and improve analysis accuracy by overcoming single-reference bias.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Natalya Yutin, Sean Benler, Sergei A. Shmakov, Yuri Wolf, Igor Tolstoy, Mike Rayko, Dmitry Antipov, Pavel A. Pevzner, Eugene Koonin
Summary: Analyzing 4907 Circular Metagenome Assembled Genomes from human microbiomes, researchers identified and characterized nearly 600 diverse genomes of crAss-like phages, revealing two potential families with unusual genomic features, including high density of self-splicing introns and inteins.
NATURE COMMUNICATIONS
(2021)
Review
Biochemical Research Methods
Yuansheng Liu, Xiangzhen Shen, Yongshun Gong, Yiping Liu, Bosheng Song, Xiangxiang Zeng
Summary: This paper discusses the importance of the SAM format file and related tools for sequencing analysis. It introduces the format of SAM and the overall process of sequencing analysis. It also categorizes existing work and explores the relevant tools, and provides a summary and future directions.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Charlotte Tumescheit, Andrew E. Firth, Katherine Brown
Summary: Multiple sequence alignments (MSAs) are critical for biological investigation, but they are often affected by incomplete and divergent sequences. To solve this issue, we have developed a comprehensive and user-friendly MSA trimming tool that offers various visualisation options, allowing users to intervene and understand the removed content.
Article
Biochemical Research Methods
Kieran Boyce, Fabian Sievers, Desmond G. Higgins
ALGORITHMS FOR MOLECULAR BIOLOGY
(2015)
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Biochemical Research Methods
Gearoid Fox, Fabian Sievers, Desmond G. Higgins
Article
Biochemistry & Molecular Biology
Thomas Schwarzl, Desmond G. Higgins, Walter Kolch, David J. Duffy
JOURNAL OF MOLECULAR BIOLOGY
(2015)
Letter
Multidisciplinary Sciences
Kieran Boyce, Fabian Sievers, Desmond G. Higgins
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Article
Oncology
David J. Duffy, Aleksandar Krstic, Melinda Halasz, Thomas Schwarzl, Dirk Fey, Kristiina Iljin, Jai Prakash Mehta, Kate Killick, Jenny Whilde, Benedetta Turriziani, Saija Haapa-Paananen, Vidal Fey, Matthias Fischer, Frank Westermann, Kai-Oliver Henrich, Steffen Bannert, Desmond G. Higgins, Walter Kolch
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Biochemistry & Molecular Biology
Susan F. Fitzpatrick, Zsolt Fabian, Bettina Schaible, Colin R. Lenihan, Thomas Schwarzl, Javier Rodriguez, Xingnan Zheng, Zongwei Li, Murtaza M. Tambuwala, Desmond G. Higgins, Yvonne O'Meara, Craig Slattery, Mario C. Manresa, Peter Fraisl, Ulrike Bruning, Myriam Baes, Peter Carmeliet, Glen Doherty, Alex von Kriegsheim, Eoin P. Cummins, Cormac T. Taylor
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2016)
Article
Biochemistry & Molecular Biology
Peter Jehl, Jean Manguy, Denis C. Shields, Desmond G. Higgins, Norman E. Davey
NUCLEIC ACIDS RESEARCH
(2016)
Article
Multidisciplinary Sciences
Paul D. Donovan, Markus S. Schroeder, Desmond G. Higgins, Geraldine Butler
Article
Oncology
David J. Duffy, Aleksandar Krstic, Thomas Schwarzl, Melinda Halasz, Kristiina Iljin, Dirk Fey, Bridget Haley, Jenny Whilde, Saija Haapa-Paananen, Vidal Fey, Matthias Fischer, Frank Westermann, Kai-Oliver Henrich, Steffen Bannert, Desmond G. Higgins, Walter Kolch
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Genetics & Heredity
Markus S. Schroder, Kontxi Martinez de San Vicente, Tamara H. R. Prandini, Stephen Hammel, Desmond G. Higgins, Eduardo Bagagli, Kenneth H. Wolfe, Geraldine Butler
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Biochemistry & Molecular Biology
Fabian Sievers, Desmond G. Higgins
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Biochemical Research Methods
Fabian Sievers, Desmond G. Higgins
Article
Biochemical Research Methods
Quan Le, Fabian Sievers, Desmond G. Higgins