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

Description

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 Conference Topics Organization Contents BDDBlast—A Memory Efficient Architecture for Pairwise Alignments 1 Introduction 2 System and Methods 2.1 The Gapped BLAST Algorithm 2.2 Binary Decision Diagrams (BDDs) 3 Algorithm 4 Implementation 4.1 Databases and Sequences Tested 5 Discussion 5.1 Efficient Memory Usage 5.2 Faster Execution Time 6 Conclusion References Scientific Workflow Interactions: An Application to Cancer Gene Identification 1 Introduction 2 Methods 2.1 Workflow Abstraction 2.2 Choosing SWfMS 2.3 Interactions 3 Results 3.1 Architecture 4 Conclusions References Accuracy of RNA Structure Prediction Depends on the Pseudoknot Grammar 1 Introduction 2 Algebraic Dynamic Programming and ADPfusion 3 Pseudoknot Grammars 4 Computational Experiments 5 Availability 6 Concluding Remarks References Comparison of Machine Learning Pipelines for Gene Expression Matrices 1 Introduction 2 Methodology 3 Experiments and Results 3.1 Dataset 3.2 Pipeline Instantiation 3.3 Results 4 Final Remarks References Evaluating Machine Learning Models for Essential Protein Identification 1 Introduction 2 Methodology 2.1 Data Preparation 2.2 Data Training and Prediction 3 Results 4 Final Remarks References Study on the Complexity of Omics Data: An Analysis for Cancer Survival Prediction 1 Introduction 2 Related Works 3 Data Complexity Measures 4 Methodology 4.1 Collection and Preparation of Omics Data 4.2 Extraction of Data Complexity Measures 4.3 Training and Evaluation of the Predictive Models 5 Results 5.1 Complexity Measures and Classification Performance 5.2 Comparison Among Omics and Cancer Types 6 Conclusion References Identifying Large Scale Conformational Changes in Proteins Through Distance Maps and Convolutional Networks 1 Introduction 2 Methodology 2.1 Dataset 2.2 Model Building 2.3 Experimental Design 3 Results 4 Conclusions References Clustering Analysis Indicates Genes Involved in Progesterone-Induced Oxidative Stress in Pancreatic Beta Cells: Insights to Understanding Gestational Diabetes 1 Introduction 2 Problem Definition 3 Methods 3.1 Clustering Methods 3.2 Reference Modules 3.3 Validation Indices 3.4 Functional Enrichment Analysis 3.5 Microarray Experiments 4 Experimental Results 4.1 Module Detection Experiments 4.2 Functional Enrichment Analysis 5 Conclusion and Future Work References An External Memory Approach for Large Genome De Novo Assembly 1 Introduction 2 Related Works 3 de Bruijn Graph Approach Construction 3.1 Algorithm to DBG Construction 4 External Memory Processing at Last Step Analysis 5 Implementation and Preliminary Results 5.1 Number of Skipped k-mers at Each Iteration 5.2 Comparison with Other Assemblers 6 Conclusions and Future Works References Computational Methodology for Discovery of Potential Inhibitory Peptides 1 Introduction 2 Methodology 2.1 Bibliographic Survey 2.2 Catalytic Site Analysis 2.3 Catalytic Site Analysis 2.4 Sequence Filtering 2.5 Molecular Docking 2.6 Filtering the Best Models 3 Results 4 Conclusion References A Non Exhaustive Search of Exhaustiveness 1 Introduction 2 Related Work 3 Data and Simulations 3.1 Data 3.2 Simulations 3.3 Exhaustiveness 3.4 Simulation Box 4 Results 5 Discussion 6 Conclusion References Search for Zinc Complexes with High Affinity in Pyrazinamidase from Mycobacterium Tuberculosis Resistant to Pyrazinamide 1 Introduction 2 Material and Methods 2.1 Obtaining the Data 2.2 Exploratory Data Analysis About Ligands 2.3 Molecular Docking 2.4 Docking Descriptors and pKd RFL-Score 3 Results 3.1 Exploratory Data Analysis for Ligands Selection 3.2 Molecular Docking Simulations 3.3 Scoring Values: Glide and RFL-Score 4 Discussion 5 Conclusions References How Bioinformatics Can Aid Biodiversity Description: The Case of a Probable New Species of Orthonychiurus (Collembola, Hexapoda) 1 Introduction 2 Material and Methods 2.1 Sampling and RNA Extraction 2.2 Transcriptome Sequencing and Analysis 2.3 Taxonomical Confirmation 3 Results 3.1 Taxa Assignment to an Unidentified Specimen Through Transcriptome Analysis 3.2 Species Investigation 3.3 Evidence of Gene-Specific Expansions in Orthonychiurus sp. nov. 4 Conclusions References Phylogeny Trees as a Tool to Compare Inference Algorithms of Orthologs 1 Introduction 2 Methodology 3 Results and Discussion 4 Conclusion References Water Pollution Shifts the Soil and Fish Gut Microbiomes Increasing the Circulation of Antibiotic Resistance Genes in the Environment 1 Introduction 2 Material and Methods 2.1 Sampling and DNA Extraction 2.2 Metagenome Sequencing and Analysis 3 Results 3.1 Metagenomes Statistics 3.2 Taxonomic Classification 3.3 Antibiotic Resistance Genes 4 Conclusions References A 1.375-Approximation Algorithm for Sorting by Transpositions with Faster Running Time 1 Introduction 2 Sorting Distance and the Cycle Graph 3 Finding 2-Transpositions in Quadratic Time 4 O(n5) Time 1.375-Approximation Algorithm 5 Experimental Analysis 6 Conclusion References 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 1 Introduction 2 Material and Methods 2.1 Genomic Sequences 2.2 Analysis of the Genomic Potential for the Production of Specialized Metabolites 3 Results 4 Discussion References Author Index