Programa de Pós-Graduação em Computação Aplicada - PPCA/NDAE/Tucuruí
URI Permanente desta comunidadehttps://repositorio.ufpa.br/handle/2011/9398
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Navegando Programa de Pós-Graduação em Computação Aplicada - PPCA/NDAE/Tucuruí por Orientadores "VERAS, Adonney Allan de Oliveira"
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Item Acesso aberto (Open Access) Ferramenta baseada em cuckoo filter para remoção de redundância em dados de sequenciadores de segunda geração (NGS - next generation sequencing)(Universidade Federal do Pará, 2019-12-02) GAIA, Antonio Sérgio Cruz; VERAS, Adonney Allan de Oliveira; http://lattes.cnpq.br/2201652617167877; https://orcid.org/0000-0002-7227-0590The second-generation sequencing platforms, also known as NGS – Next Generation Sequencing, produce a great amount of data, which demands high complexity and computational cost in the processing of these data. These platforms generate duplicated reads that come from the preparation of the genomic library and are included in the amplification stage by PCR (Polymerase Chain Reaction). This redundancy can increase the computational requirements and processing time of subsequent analyses (for instance, de novo assembly). To reduce the computational cost of theses analyses, it is necessary to remove these reads from the data set of the sequenced organism. In this work, we present the NGSReadsTreatment, a computational tool to remove duplicated reads in paired-end or single-end data sets. The input for NGSReadsTreatment consists of reads from any sequencing platform with same or different read lengths. Its engine uses a Cuckoo Filter probabilistic structure to identify and remove redundant readings. The identification is done by comparing the reads among themselves, this way, not any pre-requisite is necessary besides the reads set. The validation of the tool was carried out by using a set of real and simulated data. To assess the efficiency of the tool, it was compared to other tools of redundancy removal. The results indicate the efficiency of the NGSReadsTreatment, for it produced the best outcome, both in the number of redundancies removed and the use of memory, in all tests done. Developed in JAVA, the NGSReadsTreatment is compatible with UNIX/Linux and Windows operating systems and has a version with a graphic interface to facilitate its use.Item Acesso aberto (Open Access) PredictmodelGUI: ferramenta para classificação de genes essenciais através de técnicas de aprendizado de máquina(Universidade Federal do Pará, 2025-06-06) MOIA, Gislenne da Silva; SILVA, Cleison Daniel; http://lattes.cnpq.br/1445401605385329; HTTPS://ORCID.ORG/0000-0001-8280-2928; VERAS, Adonney Allan de Oliveira; http://lattes.cnpq.br/2201652617167877; https://orcid.org/0000-0002-7227-0590DNA sequencing technologies have provided significant advances in the understanding of the genetic content of numerous organisms, ranging from microorganisms to humans. Among the analyses performed in the Omics Sciences, Annotation stands out as one of the most important. Conceptually, this process consists of inferring biological information from genomic sequences, which allows researchers to understand the function of genetic products, such as Genes — the Basic Units of Heredity responsible for the physical and hereditary characteristics of an organism. Some Genes perform vital functions by encoding Proteins or RNAs essential for processes such as Cellular Metabolism, which participate in crucial pathways like Glycolysis and the Tricarboxylic Acid Cycle. Sequencing Platforms have started to generate large volumes of data, which has driven advances in the Omics fields and fostered the development of computational methods aimed at diverse analyses. More recently, Machine Learning and Artificial Intelligence techniques have been applied to these data, with studies demonstrating the effectiveness of biology-inspired approaches. These models do not require rule-based programming, although their creation still demands advanced skills in Programming and Computing. To contribute toward solving this challenge, this study presents PredictModelGUI, a graphical interface developed in Python that implements nine models to classify Essential Genes. The interface allows importing datasets, re-training models, and adjusting parameters. The information is stored in the software database, which ensures traceability and provides a simple and intuitive tool to test different configurations. AvailableItem Acesso aberto (Open Access) Tecnologia assistiva para auxiliar o ensino de genética clássica a deficientes visuais: um estudo de caso na região amazônica(Universidade Federal do Pará, 2020-07-10) OLIVEIRA, Mônica Silva de; MERLIN, Bruno; http://lattes.cnpq.br/7336467549495208; VERAS, Adonney Allan de Oliveira; http://lattes.cnpq.br/2201652617167877; https://orcid.org/0000-0002-7227-0590Assistive Technologies has contributed significantly to the inclusion process, encompassing solutions that contribute to the dynamic and gradual construction of the teaching-learning process. It is possible to realize over the years the development of many computational solutions in this area for the visually impaired. However, there is also a strong need for productions in specific areas, such as Genetics, a subarea of Biological Sciences, still little explored. Analyzing this gap, the work in question proposes to make use of mobile devices as a facilitating tool in the inclusion process, through the development of an assistance application to assist in the teaching of classical genetics to students with visual impairments in the regular classroom. Allied to the mobile application, a web platform is proposed to promote and facilitate the interaction between students and professors of the discipline. Based on the survey of requirements and usability tests, through the SUS Usability Scale, the application interface was developed, according to meet the needs of the users. This study was carried out in the city of Tucuruí, the southeastern region of Pará. The results obtained in relation to the use of the application by the participants, show a high level of satisfaction (80%), also allowing it to be used by the visually impaired student to study inside and outside the school environment.