Strategies for Multiple Sequence Alignment by Hugh B. Nicholas, Alexander J. Ropelewski, David W. Deerfield

“…We present an overview of multiple sequence alignments to outline the practical consequences for the choices among different techniques and parameters. …”
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Hardware Accelerated Sequence Alignment with Traceback by Scott Lloyd, Quinn O. Snell

“…Biological sequence alignment is an essential tool used in molecular biology and biomedical applications. …”
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Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors. by René Staritzbichler, Edoardo Sarti, Emily Yaklich, Antoniya Aleksandrova, Marcus Stamm, Kamil Khafizov, Lucy R Forrest

“…Previous studies have introduced restraints as a means to impose the matching of positions during sequence alignments, originally in the context of genome assembly. …”
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Pairwise Heuristic Sequence Alignment Algorithm Based on Deep Reinforcement Learning by Yong-Joon Song, Dong Jin Ji, Hyein Seo, Gyu-Bum Han, Dong-Ho Cho

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TSTA: thread and SIMD-based trapezoidal pairwise/multiple sequence-alignment method by Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan

“… The rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman–Wunsch method introduces the foundational dynamic-programming matrix calculation for global alignment, which evaluates the overall alignment of sequences. …”
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Evaluating Sequence Alignment Tools for Antimicrobial Resistance Gene Detection in Assembly Graphs by Yusreen Shah, Somayeh Kafaie

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The Historical Evolution and Significance of Multiple Sequence Alignment in Molecular Structure and Function Prediction by Chenyue Zhang, Qinxin Wang, Yiyang Li, Anqi Teng, Gang Hu, Qiqige Wuyun, Wei Zheng

Subjects: “…pairwise sequence alignment…”
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Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega by Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D Thompson, Desmond G Higgins

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Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method by Lukas Burger, Erik van Nimwegen

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High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP by Khaled Benkrid, Ali Akoglu, Cheng Ling, Yang Song, Ying Liu, Xiang Tian

“…In particular, the paper presents the results of a comparative study between three different acceleration technologies, namely, Field Programmable Gate Arrays (FPGAs), Graphics Processor Units (GPUs), and IBM’s Cell Broadband Engine (Cell BE), in the design and implementation of the widely-used Smith-Waterman pairwise sequence alignment algorithm, with general purpose processors as a base reference implementation. …”
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Protocol Reverse Analysis of Ethernet for Control Automation Technology Based on Sequence Alignment and Pearson Correlation Coefficient by Xiaopeng Wang, Yu Yao, Zhongwei Li, Changhe Su, Yunsong Tian

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A multi-objective fuzzy model based on enhanced artificial fish Swarm for multiple RNA sequences alignment by Medhat A. Tawfeek, Ibrahim Alrashdi, Madallah Alruwaili, Gamal Farouk Elhady

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Molecular Detection and Characterization of Haemonchus spp. in Cattle in Nigeria by Olamilekan Banwo, Olalekan Jeremiah, Rofiat Adesina, Abraham Adeyemo, Olusegun Fagbohun

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Cloning and sequencing of a cucumber mosaic virus satellite RNA isolated from Raphanus sativus and comparison of its sequence with 12 satellite RNAs by CHEN Ji-shuang, FENG Ming-guang, ZHANG Yao-zhou

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MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files by Michail Patsakis, Kimonas Provatas, Aris Karatzikos, Charalampos Koilakos, Ioannis Mouratidis, Ilias Georgakopoulos-Soares

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A Comprehensive Protocol for Bayesian Phylogenetic Analysis Using MrBayes: From Sequence Alignment to Model Selection and Phylogenetic Inference by Jinxing Wang, Fangmin Chen, Xu Xiao, Xinyao Yang, Wanting Xia

“…This protocol presents an integrated workflow that leverages GUIDANCE2 for rigorous sequence alignment, ProtTest and MrModeltest for robust model selection, and MrBayes for phylogenetic tree estimation through Bayesian inference. …”
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Parallel algorithm for sensitive sequence recognition from long-read genome data with high error rate by Cheng ZHONG, Hui SUN

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Parallel algorithm for sensitive sequence recognition from long-read genome data with high error rate by Cheng ZHONG, Hui SUN

Subjects: “…sensitive sequence recognition;filtering;similarity calculation;sequence alignment;parallel computing…”
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Fast noisy long read alignment with multi-level parallelism by Zeyu Xia, Canqun Yang, Chenchen Peng, Yifei Guo, Yufei Guo, Tao Tang, Yingbo Cui

Subjects: “…Sequence alignment…”
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Analysis of General Purpose FPGA-based Development Boards Efficiency in DNA Processing Applications by SZÁSZ Csaba

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