Advances in Bioinformatics and Computational Biology : 15th Brazilian Symposium on Bioinformatics, BSB 2022, Buzios, Brazil, September 21–23, 2022, Proceedings

This book constitutes the proceedings of the 15th Brazilian Symposium on Bioinformatics on Advances in Bioinformatics and Computational Biology, BSB 2022, which took place in Buzios, Brazil, in September 2022. The 10 full papers and 7 short papers presented in this volume were carefully reviewed and selected from 23 submissions. The papers focus on bioinformatics, computational biology, Biological Databases, Biological Networks, Cheminformatics, Evolutionary Genomics, Computational Proteomics, Systems Biology, Drug Design, Genomics, Machine Learning applications in Bioinformatics, Metagenomics, Molecular Docking and Modeling, Molecular Evolution and Phylogenetics, Protein Structure and Modeling, Proteomics, Transcriptomics, Single-Cell Analysis, Workflows in Bioinformatics. Preface 6 Conference Topics 7 Organization 8 Contents 12 BDDBlast—A Memory Efficient Architecture for Pairwise Alignments 14 1 Introduction 14 2 System and Methods 15 2.1 The Gapped BLAST Algorithm 15 2.2 Binary Decision Diagrams (BDDs) 17 3 Algorithm 18 4 Implementation 21 4.1 Databases and Sequences Tested 22 5 Discussion 22 5.1 Efficient Memory Usage 22 5.2 Faster Execution Time 23 6 Conclusion 24 References 25 Scientific Workflow Interactions: An Application to Cancer Gene Identification 27 1 Introduction 27 2 Methods 28 2.1 Workflow Abstraction 28 2.2 Choosing SWfMS 29 2.3 Interactions 29 3 Results 30 3.1 Architecture 30 4 Conclusions 31 References 31 Accuracy of RNA Structure Prediction Depends on the Pseudoknot Grammar 33 1 Introduction 34 2 Algebraic Dynamic Programming and ADPfusion 35 3 Pseudoknot Grammars 38 4 Computational Experiments 40 5 Availability 41 6 Concluding Remarks 41 References 42 Comparison of Machine Learning Pipelines for Gene Expression Matrices 45 1 Introduction 45 2 Methodology 46 3 Experiments and Results 47 3.1 Dataset 47 3.2 Pipeline Instantiation 48 3.3 Results 49 4 Final Remarks 49 References 50 Evaluating Machine Learning Models for Essential Protein Identification 51 1 Introduction 51 2 Methodology 52 2.1 Data Preparation 52 2.2 Data Training and Prediction 53 3 Results 53 4 Final Remarks 55 References 56 Study on the Complexity of Omics Data: An Analysis for Cancer Survival Prediction 57 1 Introduction 57 2 Related Works 58 3 Data Complexity Measures 59 4 Methodology 60 4.1 Collection and Preparation of Omics Data 61 4.2 Extraction of Data Complexity Measures 61 4.3 Training and Evaluation of the Predictive Models 62 5 Results 62 5.1 Complexity Measures and Classification Performance 62 5.2 Comparison Among Omics and Cancer Types 65 6 Conclusion 67 References 67 Identifying Large Scale Conformational Changes in Proteins Through Distance Maps and Convolutional Networks 69 1 Introduction 69 2 Methodology 72 2.1 Dataset 72 2.2 Model Building 73 2.3 Experimental Design 76 3 Results 76 4 Conclusions 78 References 78 Clustering Analysis Indicates Genes Involved in Progesterone-Induced Oxidative Stress in Pancreatic Beta Cells: Insights to Understanding Gestational Diabetes 81 1 Introduction 81 2 Problem Definition 82 3 Methods 83 3.1 Clustering Methods 83 3.2 Reference Modules 83 3.3 Validation Indices 83 3.4 Functional Enrichment Analysis 84 3.5 Microarray Experiments 84 4 Experimental Results 84 4.1 Module Detection Experiments 84 4.2 Functional Enrichment Analysis 85 5 Conclusion and Future Work 89 References 89 An External Memory Approach for Large Genome De Novo Assembly 92 1 Introduction 92 2 Related Works 93 3 de Bruijn Graph Approach Construction 94 3.1 Algorithm to DBG Construction 94 4 External Memory Processing at Last Step Analysis 96 5 Implementation and Preliminary Results 98 5.1 Number of Skipped k-mers at Each Iteration 99 5.2 Comparison with Other Assemblers 100 6 Conclusions and Future Works 101 References 102 Computational Methodology for Discovery of Potential Inhibitory Peptides 104 1 Introduction 104 2 Methodology 105 2.1 Bibliographic Survey 105 2.2 Catalytic Site Analysis 105 2.3 Catalytic Site Analysis 105 2.4 Sequence Filtering 106 2.5 Molecular Docking 106 2.6 Filtering the Best Models 107 3 Results 107 4 Conclusion 109 References 109 A Non Exhaustive Search of Exhaustiveness 110 1 Introduction 110 2 Related Work 112 3 Data and Simulations 112 3.1 Data 112 3.2 Simulations 113 3.3 Exhaustiveness 114 3.4 Simulation Box 114 4 Results 114 5 Discussion 116 6 Conclusion 119 References 120 Search for Zinc Complexes with High Affinity in Pyrazinamidase from Mycobacterium Tuberculosis Resistant to Pyrazinamide 122 1 Introduction 123 2 Material and Methods 124 2.1 Obtaining the Data 125 2.2 Exploratory Data Analysis About Ligands 125 2.3 Molecular Docking 125 2.4 Docking Descriptors and pKd RFL-Score 126 3 Results 126 3.1 Exploratory Data Analysis for Ligands Selection 126 3.2 Molecular Docking Simulations 127 3.3 Scoring Values: Glide and RFL-Score 127 4 Discussion 130 5 Conclusions 131 References 132 How Bioinformatics Can Aid Biodiversity Description: The Case of a Probable New Species of Orthonychiurus (Collembola, Hexapoda) 134 1 Introduction 134 2 Material and Methods 135 2.1 Sampling and RNA Extraction 135 2.2 Transcriptome Sequencing and Analysis 135 2.3 Taxonomical Confirmation 136 3 Results 136 3.1 Taxa Assignment to an Unidentified Specimen Through Transcriptome Analysis 136 3.2 Species Investigation 137 3.3 Evidence of Gene-Specific Expansions in Orthonychiurus sp. nov. 138 4 Conclusions 139 References 139 Phylogeny Trees as a Tool to Compare Inference Algorithms of Orthologs 141 1 Introduction 141 2 Methodology 143 3 Results and Discussion 145 4 Conclusion 150 References 150 Water Pollution Shifts the Soil and Fish Gut Microbiomes Increasing the Circulation of Antibiotic Resistance Genes in the Environment 153 1 Introduction 153 2 Material and Methods 154 2.1 Sampling and DNA Extraction 154 2.2 Metagenome Sequencing and Analysis 154 3 Results 154 3.1 Metagenomes Statistics 154 3.2 Taxonomic Classification 155 3.3 Antibiotic Resistance Genes 156 4 Conclusions 157 References 158 A 1.375-Approximation Algorithm for Sorting by Transpositions with Faster Running Time 160 1 Introduction 160 2 Sorting Distance and the Cycle Graph 161 3 Finding 2-Transpositions in Quadratic Time 163 4 O(n5) Time 1.375-Approximation Algorithm 167 5 Experimental Analysis 168 6 Conclusion 169 References 170 In Silico Analysis of the Genomic Potential for the Production of Specialized Metabolites of Ten Strains of the Bacillales Order Isolated from the Soil of the Federal District, Brazil 171 1 Introduction 171 2 Material and Methods 172 2.1 Genomic Sequences 172 2.2 Analysis of the Genomic Potential for the Production of Specialized Metabolites 172 3 Results 173 4 Discussion 174 References 175 Author Index 177