A survey of the Sli gene in wild and cultivated potato by Mercedes Ames, Andy Hamernik, William Behling, David S. Douches, Dennis A. Halterman, Paul C. Bethke

“…To learn more about Sli diversity and function in wild species relatives of cultivated potato, we obtained Sli gene sequences that extended from the 5′UTR to the 3′UTR from 133 individuals from 22 wild species relatives of potato and eight diverse cultivated potato clones. DNA sequence alignment and phylogenetic trees based on genomic and protein sequences show that there are two highly conserved groups of Sli sequences. …”
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Detection of Dengue Virus-Specific IgM and IgG Antibodies through Peptide Sequences of Envelope and NS1 Proteins for Serological Identification by Pradeep Kumar Nagar, Deepali Savargaonkar, Anupkumar R. Anvikar

“…Sequence homologies of peptides with other Flavivirus were checked by Multiple Sequence Alignment Tool ClustalX2. Peptide sequences were synthesized chemically by solid-phase peptide synthesis technique. …”
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Surveillance of SARS-CoV-2 variants in Henan, China from 2023 to 2024 by Yun Song, Bicong Wu, Hongxia Ma, Yafei Li, Su Yan, Jingjing Pan, Haifeng Wang, Ying Ye, Xueyong Huang, Wanshen Guo

“…Genome sequence analysis was performed with CLC Genomics Workbench, and genotyping and sequence alignment were carried out using the Nextclade platform. …”
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Prevalence and Molecular Characterization of Cysticercus tenuicollis Isolated from Some Intermediate Host in Kurdistan-Iraq by Abdullah Ahmed Hama, Rostam Hama Zorab, Fatima Mohammed Ali, Awaz M. Salih, Amer Abdullah Hassan

“…The nucleotide sequence alignment of cytochrome oxidase subunit 1 (CO 1) gene revealed that the amplified DNA fragment is belong to Taenia hydatigena and Echinococcus granulosus and the nucleotide sequences of T. hydatigena deposited in GenBank under accession number (MH638348). …”
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The Chloroplastic Small Heat Shock Protein Gene KvHSP26 Is Induced by Various Abiotic Stresses in Kosteletzkya virginica by Xiaohua Liu, Lizi Zhao, Jianzhao Li, Lijun Duan, Kai Zhang, Xuqiang Qiao, Weihuan Li, Chengchao Zheng, Xiaoli Tang, Hongxia Zhang

“…Bioinformatics analyses revealed that KvHSP26 encoded a chloroplastic protein with the typical features of sHSPs. Amino acid sequence alignment and phylogenetic analysis demonstrated that KvHSP26 shared 30%-77% homology with other sHSPs from Arabidopsis, cotton, durian, salvia, and soybean. …”
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The Association between Deoxyribonucleic Acid Hypermethylation in Intron VII and Human Leukocyte Antigen-C∗07 Expression in Patients with Endometriosis by Wenrong Zhao, Lei Lei, Rui Chen, Yanmin Zhang, Linlin Chang, Jingxin Cheng

“…The test screened methylation-differentiated 5′–C–phosphate–G–3′ (CpG) sites and then located the target genes affected by these sites following sequence alignment. Then, an additional 22 patients and 26 healthy controls were enrolled to further verify the difference in the selected genes between endometriosis patients and healthy women. …”
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Development of Genome-Wide Unique Indel Markers for a Heat-Sensitive Genotype in Wheat (<i>Triticum aestivum</i> L.) by Huijie Zhai, Kunpeng Xu, Meng Wang, Zhenchuang Wang, Ziyang Cai, Ao Li, Anxin He, Xiaoming Xie, Lingling Chai, Mingjiu Liu, Xingqi Ou, Zhongfu Ni

“…These primer pairs are believed to be unique and polymorphic in the wheat genome; as gathered from the evidence, (i) 76.18 to 99.34% of the 11,016 primer pairs yielded a single hit during sequence alignment with 18 sequenced genomes, (ii) 83.59 to 90.98% of 1042 synthesized primer pairs amplified a single band in 16 wheat accessions, and (iii) 59.69 to 99.81% of the tested 1042 primer pairs were polymorphic between E6015-3S and 15 individual wheat accessions. …”
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High Antennal Expression of <i>CYP6K1</i> and <i>CYP4V2</i> Participate in the Recognition of Alarm Pheromones by <i>Solenopsis invicta</i> Buren by Xinyi Jiang, Jiacheng Shen, Peng Lin, Youming Hou

“…To understand whether the highly expressed CYPs in the antennae play an olfactory function in <i>Solenopsis invicta</i> worker, in this study, we find six highly expressed antennal CYPs from the transcriptome of <i>S. invicta</i>. Multiple sequence alignment and phylogenetic analysis divided them into two families: the CYP3 family (<i>SinvCYP6K1</i>, <i>SinvCYP6K1-1</i>) and the CYP4 family (<i>SinvCYP4C1</i>, <i>SinvCYP4C1-1</i>, <i>SinvCYP4C1-2</i>, <i>SinvCYP4V2</i>). …”
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Development of a 50K SNP array for whole-genome analysis and its application in the genetic localization of eggplant (Solanum melongena L.) fruit shape by Chuying Yu, Qihong Yang, Weiliu Li, Yaqin Jiang, Guiyun Gan, Liangyu Cai, Xinchun Li, Zhiqiang Li, Wenjia Li, Min Zou, Yang Yang, Yikui Wang

“…The BSA-seq data were located in the 78444173−84449348 interval on chromosome 3, with a size of 6 Mb, which was narrowed to 712.6 kb through fine mapping. Further sequence alignment and expression analysis revealed SmIQD14 as a candidate gene controlling eggplant fruit shape. …”
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Understanding the clinical and molecular epidemiological characteristics of carbapenem-resistant Acinetobacter baumannii infections within intensive care units of three teaching ho... by Pengyu Zhang, Jingchen Hao, Yafen Zhang, Junfeng Su, Guozhuang Sun, Jun Xie, Jian Hu, Guocai Li

“…Acquired antimicrobial resistance genes and virulence factors carried in the isolated group genome were analyzed by ResFinder, PubMLST and VFDB. Sequence alignment was used to analyze genetic environment around bla OXA−23. …”
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Diversity in mitotic DNA repair efficiencies between commercial inbred maize lines and native Central American purple landraces by Carlos Víquez-Zamora, Sergio Castro-Pacheco, María Viñas, Pablo Bolaños-Villegas

“…The kinase gene ZeaATM1 was amplified and sequenced in B73, Mo17, P1 and P2. Multiple sequence alignment of DNA and aminoacid sequences was performed using ClustalW. …”
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Detection of 5 Kinds of Genes Related to Plasmid-Mediated Quinolone Resistance in Four Species of Nonfermenting Bacteria with 2 Drug Resistant Phenotypes by De-Song Ming, Qing-Qing Chen, Xiao-Ting Chen

“…The amplified products were analyzed by 1% agarose gel electrophoresis and sequenced. Sequence alignment was carried out using the bioinformatics technique. …”
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Transcriptome Analysis of <i>Stephania yunnanensis</i> and Functional Validation of CYP80s Involved in Benzylisoquinoline Alkaloid Biosynthesis by Wenlong Shi, Qishuang Li, Xinyi Li, Linglong Luo, Jingyi Gan, Ying Ma, Jian Wang, Tong Chen, Yifeng Zhang, Ping Su, Xiaohui Ma, Juan Guo, Luqi Huang

“…We then identified candidate genes through functional annotation and sequence alignment and further analyzed them in combination with the genome. …”
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Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? by Robert Lücking, M. Catherine Aime, Barbara Robbertse, Andrew N. Miller, Hiran A. Ariyawansa, Takayuki Aoki, Gianluigi Cardinali, Pedro W. Crous, Irina S. Druzhinina, David M. Geiser, David L. Hawksworth, Kevin D. Hyde, Laszlo Irinyi, Rajesh Jeewon, Peter R. Johnston, Paul M. Kirk, Elaine Malosso, Tom W. May, Wieland Meyer, Maarja Öpik, Vincent Robert, Marc Stadler, Marco Thines, Duong Vu, Andrey M. Yurkov, Ning Zhang, Conrad L. Schoch

“…Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. …”
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Expression Analysis and SNP Mining of the Parkin Co-Regulated Gene (PACRG) and parkin in Penaeus vannamei Against White Spot Syndrome Virus by Qian XUE, Xupeng LI, Yang LI, Sheng LUAN, Kun LUO, Jie KONG, Qun XING, Xianhong MENG

“…Parkin is predicted to contain UBQ and IBR structural domains and a signal peptide structure. Amino acid sequence alignment and phylogenetic tree analysis showed that the homology of PACRG between P. vannamei and Penaeus japonicus was the highest at 89.70% similarity. …”
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Identification and expression analysis of the heat shock proteins Hsp70, Hsp90, and Hsp90b in Litopenaeus vannamei under low-temperature stress by Min Peng, Hui Wang, Shuiping Wen, Zheng Liang, Zheng Huang, Bin Zhang, Tianchong Chen, Qingyun Liu, Qiangyong Li, Yuan Meng, Yuliu Huang, Chunling Yang, Digang Zeng, Manyuan Li, Weilin Zhu, Yongzhen Zhao

“…Additionally, the survival rate of L. vannamei significantly decreased following hsp90 knockdown. DNA sequence alignment identified 12 single nucleotide polymorphisms (SNPs) in the hsp70 gene and 17 SNPs in the hsp90 gene. …”
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New Hosts of Simplicimonas similis and Trichomitus batrachorum Identified by 18S Ribosomal RNA Gene Sequences by Kris Genelyn B. Dimasuay, Orlie John Y. Lavilla, Windell L. Rivera

“…Genomic DNA was extracted using Chelex method and the 18S rRNA gene was successfully amplified through novel sets of primers and undergone DNA sequencing. Aligned isolate sequences together with retrieved 18S rRNA gene sequences of known trichomonads were utilized to generate phylogenetic trees using maximum likelihood and neighbor-joining analyses. …”
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The SsDREB Transcription Factor from the Succulent Halophyte Suaeda salsa Enhances Abiotic Stress Tolerance in Transgenic Tobacco by Xu Zhang, Xiaoxue Liu, Lei Wu, Guihong Yu, Xiue Wang, Hongxiang Ma

“…This protein was classified in the A-6 group of DREB subfamily based on multiple sequence alignments and phylogenetic characterization. Yeast one-hybrid assays showed that SsDREB protein specifically binds to the DRE sequence and could activate the expression of reporter genes in yeast, suggesting that the SsDREB protein was a CBF/DREB transcription factor. …”
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hsa-miR-548d-3p: a potential microRNA to target nucleocapsid and/or capsid genes in multiple members of the Flaviviridae family by H. W. Cayatineto, S. T. Hakim

“…In the current study, we used bioinformatic tools to predict a possible miRNA sequence that could be complementary to the nucleocapsid (NP) and/or capsid (CP) gene of the Flaviviridae family and provide an inhibitory solution.MethodsBioinformatics is a field of science that includes tremendous computational analysis, logarithms, and sequence alignments. To predict the right alignments between miRNA and viral mRNA genomes, we used computational databases such as miRBase, NCBI, and Basic Alignment Search Tool–nucleotides (BLAST-n).ResultsOf the 2,600 mature miRNAs, hsa-miR-548d-3p revealed complementary sequences with the flavivirus capsid gene and bovine viral diarrhea virus (BVDV) capsid gene and was selected as a possible candidate to inhibit flaviviruses.ConclusionAlthough more detailed in vitro and in vivo studies are required to test the possible inhibitory effects of hsa-miR-548d-3p against flaviviruses, this computational study may be the first step to study further, developing a novel therapeutic for lethal viruses within the Flaviviridae family using suggested candidate miRNAs.…”
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Genetic Relationships Analysis of Some various Species Using Cytochrome b Genes as a Phylogenetic Marker by Lajan Salahaldin Ahmed

“…PCR amplification of the mitochondrial Cyt-b gene resulted in an approximately 358 bp amplicon in size for all species, and sequences alignment and phylogenetic analyses were performed with Bio Edit and MEGA X software’s to determine genetic similarities and distances. …”
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