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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Identification and characterization of multiple novel viruses in fecal samples of cormorants by Li Ji, Li Ji, Ran Zhao, Yifei Pei, Yijie Sun, Xiaoyi Sun, Likai Ji, Xiaochun Wang, Yuwei Liu, Quan Shen, Shixing Yang, Yan Wang, Wen Zhang

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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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Resolving the source of branch length variation in the Y chromosome phylogeny by Yaniv Swiel, Janet Kelso, Stéphane Peyrégne

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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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Research on discovering multi-step attack patterns based on clustering IDS alert sequences by MEI Hai-bin1, GONG Jian1, ZHANG Ming-hua2

“…A method of discovering multi-step attack patterns from alert data was studied.Alert similarity function was defined to construct the set of attack activity sequences.Sequence alignment technology was used to cluster the similar attack activity sequences.Multi-step attack patterns in a cluster were automatically discovered by the longest common subsequence extraction algorithm based on the idea of dynamic programming.The proposed method didn’t depend on large amounts of prior knowledge.Few configuration parameters were needed and it was easy to implement.Experimental results demonstrate the effectiveness of proposed method.…”
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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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Transforming Weakness into Strength: Improving Unreliable Malware Detection Methods by Pavel Novak, Vaclav Oujezsky

“…Key contributions include a novel combination of unreliable IoCs with sequence alignment methods, an extensive mapping study of detection techniques, and initial experiments on a dataset of over 19,000 malware samples. …”
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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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Phylobook: a tool for display, clade annotation and extraction of sequences from molecular phylogenies by Jeffrey C Furlong, Peter D Darley, Wenjie Deng, James I Mullins, Roger E Bumgarner

“…Starting with a sequence alignment file, Phylobook generates and displays phylogenetic trees adjacent to highlighter plots showing the position of mutations, and allows the user to identify lineages and recombinants, annotate and export selected subsets of sequences for downstream analysis. …”
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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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