Formulation and Analysis of Patterns in a Score Matrix for Global Sequence Alignment by James Owusu Asare, Justice Kwame Appati, Kwaku Darkwah

“…Global sequence alignment is one of the most basic pairwise sequence alignment procedures used in molecular biology to understand the similarity that arises among the structure, function, or evolutionary relationship between two nucleotide sequences. …”
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A Novel Partial Sequence Alignment Tool for Finding Large Deletions by Taner Aruk, Duran Ustek, Olcay Kursun

“…Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. …”
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X-Mapper: fast and accurate sequence alignment via gapped x-mers by Jeffry M. Gaston, Eric J. Alm, An-Ni Zhang

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Author Correction: X-Mapper: fast and accurate sequence alignment via gapped x-mers by Jeffry M. Gaston, Eric J. Alm, An-Ni Zhang

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A Primer for Disease Gene Prioritization Using Next-Generation Sequencing Data by Shuoguo Wang, Jinchuan Xing

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Genome‐Wide Analysis of the APETALA2/Ethylene‐Responsive Factor Gene Family in Carthamus tinctorius L. by Zheng‐Wei Tan, Dan‐Dan Lu, Yong‐Liang Yu, Lei Li, Lan‐Jie Xu, Wei Dong, Chun‐Ming Li, Qing Yang, Hui‐Zhen Liang

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Decoding MexB efflux pump genes: structural, molecular, and phylogenetic analysis of multidrug-resistant and extensively drug-resistant Pseudomonas aeruginosa by Muhammad Bilal Habib, Naseer Ali Shah, Afreenish Amir, Huda Ahmed Alghamdi, Muhammad Haseeb Tariq, Kiran Nisa, Mariam Ammoun

“…Protein domain architecture revealed that MexB gene proteins were involved in particular efflux pump function. Protein sequences aligned by multiple sequence alignment revealed conserved regions and sequence variants, which suggested antibiotic translocation and evolutionary divergence. …”
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Numerical Characterization of DNA Sequence Based on Dinucleotides by Xingqin Qi, Edgar Fuller, Qin Wu, Cun-Quan Zhang

“…In order to make quantitative comparisons, one devises mathematical descriptors that capture the essence of the base composition and distribution of the sequence. Alignment methods and graphical techniques (where each sequence is represented by a curve in high-dimension Euclidean space) have been used popularly for a long time. …”
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Species-Specific Gene, spt5, in the Qualitative and Quantitative Detection of Boletus reticulatus by Zhan Lei, Chen Zhang, Yinjiao Li, Lunzhao Yi, Ying Shang

“…A commercial kit was used to extract the DNA of various fungi, and the quality of DNA was determined by using universal fungus primers. Through sequence alignment, the spt5 gene was selected as the species-specific gene of B. reticulatus. …”
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Comparative Inference of Duplicated Genes Produced by Polyploidization in Soybean Genome by Yanmei Yang, Jinpeng Wang, Jianyong Di

“…Polyploidy is a widespread and recursive phenomenon during plant evolution, and it could generate massive duplicated genes which is an important resource for genetic innovation. Improved sequence alignment criteria and statistical analysis are used to identify and characterize duplicated genes produced by polyploidization in soybean. …”
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A Protein Sequence Analysis Hardware Accelerator Based on Divergences by Juan Fernando Eusse, Nahri Moreano, Alba Cristina Magalhaes Alves de Melo, Ricardo Pezzuol Jacobi

“…This stage discards poorly aligned sequences with a low similarity score and forwards sequences with good similarity scores to software, where they are reprocessed to generate the sequence alignment. In order to reduce the software reprocessing time, this work proposes a hardware accelerator for the Viterbi algorithm which includes the concept of divergence, in which the region of interest of the dynamic programming matrices is delimited. …”
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Using In Silico Methods to Identify Protein Tyrosine Kinase A (PtkA) Homolog in Non-Tuberculous Mycobacteria (NTM) by Swati Jaiswal, Sanjay Kumar

“…In silico approaches, which utilize computational tools for sequence alignment, structure prediction, and functional annotation, offer a powerful means to identify homologous proteins across different species. …”
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The Effects of Different Representations on Static Structure Analysis of Computer Malware Signatures by Ajit Narayanan, Yi Chen, Shaoning Pang, Ban Tao

“…We show that, if malware signatures are represented as artificial protein sequences, it is possible to apply standard sequence alignment techniques in bioinformatics to improve accuracy of distinguishing between worm and virus signatures. …”
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ClpB chaperone as a promising target for antimicrobial therapy: A narrative review by Sachini J. Udari, Sayoka Shamodhi, Rumesh M. Nelumdeniya, Udayana Ranatunga, Nimesha N. Senadeera, Chathuranga B. Ranaweera

“…Relevant research findings were compiled using academic databases, and data analysis was performed using Clustal Omega Multiple Sequence Alignment and Boxshade tools.…”
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Evolutionary Pattern of Asian HIV-1 Subtype B from 1990 to 2007: In Silico Analysis Based on Envelop Protein by Sobia Kanwal, Tariq Mahmood

“…An online available tool Drawgram was used for multiple sequence alignment (MSA) of HIV-1 subtype B envelop region and V3 loop while the alignment was rechecked by using CLUSTAL W and further was analyzed for GPGX motif and conserved region in V3 loop. …”
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NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation by Yuki Kagaya, Zicong Zhang, Nabil Ibtehaz, Xiao Wang, Tsukasa Nakamura, Pranav Deep Punuru, Daisuke Kihara

“…Analyses of individual components in the NuFold pipeline indicated that the performance improved by utilizing metagenome sequences for multiple sequence alignment and increasing the number of recycling. …”
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A Comprehensive Methodological Review of Major Developments in Bioinformatics Pipelines for Transcriptomic Data Analysis by Awais ALi, Syed Luqman Ali, Abdelkarem Omneya

“…Results: We examine how well different methods work under various experimental conditions and discuss important factors such as data quality, sequence alignment, data visualization, identifying gene expression differences, and data standardization. …”
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Construction of a pathogenic microorganism detection method based on third-generation nanopore sequencing data by Guoqin Mai, Jiayi Chen, Min Zhang, Wanyue Zhang, Yuting Luo, Ying Dai

“…First, a comprehensive and penetrating reference database of nucleic acids from pathogenic microorganisms was constructed, and sequence alignment analysis was performed via nanopore sequencing of metagenomic data collected from 40 patients with lower respiratory tract infection symptoms. …”
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A Nonsynonymous Single-nucleotide Polymorphism in SLC24A5 Regulates Feather Pigment Deposition in Chinese Yellow Quail by Xiaohui Zhang, Fanghu Wu, Yanxia Qi, Yuanyuan Shang, Lingyun Fan, Yifei Wang

“…Potential single-nucleotide polymorphisms (SNPs) were screened using multiple sequence alignment. The screened nonsynonymous SNPs were genotyped across 265 Chinese yellow quails using the kompetitive allele-specific PCR method. …”
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Prevalence of Ticks Infesting Dairy Cattle and the Pathogens They Harbour in Smallholder Farms in Peri-Urban Areas of Nairobi, Kenya by Shepelo Getrude Peter, Hellen Wambui Kariuki, Gabriel Oluga Aboge, Daniel Waweru Gakuya, Ndichu Maingi, Charles Matiku Mulei

“…Sequencing of the amplicons and subsequent BLASTn analysis, multiple sequence alignment, and phylogenetic reconstruction were performed to confirm the species of the pathogens. …”
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