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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Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction. by Akash Bahai, Chee Keong Kwoh, Yuguang Mu, Yinghui Li

“…Our aim is to identify factors influencing performance variation, such as RNA family diversity, sequence length, RNA type, multiple sequence alignment (MSA) quality, and deep learning model architecture. …”
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A generative adversarial network for multiple reads reconstruction in DNA storage by Xiaodong Zheng, Ranze Xie, Xiangyu Yao, Yanqing Su, Ling Chu, Peng Xu, Wenbin Liu

“…Different from previous error-correction and multiple sequence alignment methods, we first transform the multiple reads into a noisy mage, and then construct a conditional generative adversarial network to produce a “smooth” image which refers to the consensus sequence. …”
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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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Detection of circular permutations by Protein Language Models by Yue Hu, Bin Huang, Chun Zi Zang, Jia Jie Xu

“…However, many current Protein Language Model-based alignment methods, which rely on sequence alignment algorithms like the Smith-Waterman algorithm, face significant difficulties when dealing with circular permutation (CP) due to their dependency on linear sequence order. …”
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A Fused Multiscale Pictorial Sequence Learning Mechanism Applied to Pavement Detection by Zhang Jiazhen, Wang Xiulai, Zhao Shuxu

“…Using the SVM classifier with the global sequence alignment algorithm as the main kernel function, the data classification module detects anomalies, so that the algorithm can mine valuable feature attributes from multiple angles as much as possible while stably exerting its classification function. …”
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Overexpression of CsBRC, an F‐box gene from Camellia sinensis, increased the plant branching in tobacco and rice by Bokun Zhou, Qi Sheng, Xinzhuan Yao, Tong Li, Litang Lu

“…In previous work focused on GWAS that detecting GWAS signals related to plant architecture through whole genome re‐sequencing of ancient tea plants, a gene locus TEA 029928 significantly related to plant type was found. Sequence alignment results showed that this gene belonged to the F‐box family. …”
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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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Genome-wide identification and expression analysis of the WRKY gene family in Mikania micrantha by Zihan Zhang, Mei Ji, Sangzi Ze, Wenzheng Song, Bin Yang, Ning Zhao

“…Based on phylogenetic relationships, sequence alignment, and structural domain diversity, the MmWRKY gene family was preliminarily classified into three major groups and five subgroups: Group I, Group II (II-a, II-b, II-c, II-d, II-e), and Group III. …”
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Repurposing antiviral drugs targeting the PARP-1 and HER2 pathways with multifaceted impacts through integrated network analysis and molecular mechanics by Uma Maheshwari Mugundan, Praveen Sekar, Rajanandh Muhasaparur Ganesan

“…Through the application of network pharmacology, gene ontology, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, this study identified Human Epidermal Growth Factor Receptor 2 (HER2) and Poly [ADP ribose] polymerase 1(PARP-1) as key targets involved in the molecular pathways associated with breast cancer. Protein sequence alignment further revealed conserved and semi-conserved amino acid regions, including residues such as Arginine (ARG), Aspartic acid (ASP), and Phenylalanine (PHE), offering valuable insights into the structural characteristics of the target proteins. …”
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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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Genome-Wide Identification and Characterization of the LRR-RLK Gene Family in Two Vernicia Species by Huiping Zhu, Yangdong Wang, Hengfu Yin, Ming Gao, Qiyan Zhang, Yicun Chen

“…Here, we identified 236 and 230 LRR-RLKs in two industrial oil-producing trees: Vernicia fordii and Vernicia montana, respectively. Sequence alignment analyses showed that the homology of the RLK domain (23.81%) was greater than that of the LRR domain (9.51%) among the Vf/VmLRR-RLKs. …”
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Detection of Mycoplasma spp. from snakes from five different families by Marline M. Faulhaber, Florence Tardy, Franziska Saul, Elisabeth Müller, Michael Pees, Rachel E. Marschang

“…The detected bacteria can be divided into at least 6 genetically diverse clusters representing different genera and species based on multiple sequence alignment and phylogenetic analysis. Conclusions These results show that diverse mycoplasmas are found in pythons and other snakes. …”
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Studies on banana for propagation, conservation and genome analysis by Susmita Shukla, Ritambhara Bhutani, Nibha Gupta, Shiv Kant Shukla, Taramla Raman, Mohamed A. El-Sheikh, Hosam O. Elansary, Ihab Mohamed Moussa

“…DNA barcoding using Internal Transcribed Spacer1 (ITS1) markers facilitated the molecular analysis and sequence alignment of these Musa species, which illustrated their genetic relationships. …”
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Analysis of expression and transport activity of sugar transporter gene HpSWEET7 from red pitaya by ZHENG Qianming, YAN Shuang, XIE Pu, WANG Honglin, MA Yuhua

“…[Methods] HpSWEET7 gene was isolated from ‘Zihonglong’, and sequence alignment and phylogenetic relationship were analyzed. …”
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Genome-wide development of simple sequence repeat (SSR) markers at 2-Mb intervals in lotus (Nelumbo Adans.) by Fengluan Liu, Lin Xi, Naifeng Fu

“…., Chr.1-2.5, 4.5, 6.5 Mb) through four steps: online primer design, primer pair evaluation, agarose gel electrophoresis testing using six Asian lotus, one American lotus, and two their hybrids, and DNA sequence alignment. Finally, the polymerase chain reaction (PCR) efficiency of several SSR markers was validated in 20 Asian temperate lotus, eight Asian tropical lotus, and one American lotus. …”
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Genome-Wide Identification of miRNAs in Oily Persimmon (<i>Diospyros oleifera</i> Cheng) and Their Functional Targets Associated with Proanthocyanidin Metabolism by Meng Zhang, Rong Wu, Xinlong Hu, Zhengrong Luo, Qinglin Zhang, Sichao Yang

“…In our study, we identified genome-wide microRNAs (miRNAs) and their precursor sequence based on the chromosome-scale genome of oily persimmon and the miRNA database of “Eshi 1” according to the sequence alignment and secondary structure accession. The targets were predicted on the psRNATarget software based on the genome CDS database. …”
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Complete Genome Sequence and Comparative Genome Analysis of Variovorax sp. Strains PAMC28711, PAMC26660, and PAMC28562 and Trehalose Metabolic Pathways in Antarctica Isolates by Prasansah Shrestha, Jayram Karmacharya, So-Ra Han, Jun Hyuck Lee, Hyun Park, Tae-Jin Oh

“…The trehalose metabolic pathway was analyzed via bioinformatics tools, such as the dbCAN2 Meta server, Prokka annotation, Multiple Sequence Alignment, ANI calculator, and PATRIC database, which helped to predict trehalose biosynthesis and degradation genes’ involvement in the complete genome of Variovorax strains. …”
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