Prediction of new gene products and characterization of hypothetical proteins of Bifidobacterium breve DS15-17 In Silico / Predição de novos produtos gênicos e caracterização de proteínas hipotéticas de Bifidobacterium breve DS15-17 In Silico

The representation of the gene content of an organism is impacted by several factors, ranging from sampling to sequencing and then the genome assembly task. The genome assembly process can generate errors that are related to insufficient coverage in the data set, an inadequate assembly methodology, and finally, errors related to the limitation of the assembly software used. Thus, some genes remain unidentified both in complete and draft genomes, this incomplete gene knowledge impacts on several organisms, mainly of medical and industrial interest, such as Bifidobacterium breve, a Gram-positive bacterium, found in the gastrointestinal microbiota of mammals, including humans, and has beneficial probiotic activities. Therefore, the objective of this work is to identify the new gene products not represented in the genome of Bifidobacterium breve DS15-17 using the raw reads of this organism. The reads were produced from the sequencing with the Illumina MiSeq platform. PAN2HGENE software was used to identify new gene products. After the analysis, 44 new gene products were identified, 26 with described function and 18 hypothetical proteins. The hypothetical proteins identified were analyzed in the ProtoNet and Superfamily databases

O uso de sistemas de informação em saúde nos hospitais públicos do brasil: uma revisão sistemática

Objetivo: Este artigo tem como objetivo investigar a atual situação acerca do Registro de informações dos pacientes (SIS) nos hospitais públicos municipais, tendo por subsídio experiências relatadas na literatura científica. Métodos: Estudo exploratório com base em revisão sistemática da literatura. Resultados. Destaca-se o uso de diversos SIS nos hospitais públicos do Brasil, porém observa-se que todos são utilizados para processamento de dados financeiros e notificação de doenças, e surtos epidemiológico, fazendo-se necessário Sistemas direcionados para registro de informações dos pacientes (Prontuário Eletrônico do Paciente - PEP). Conclusão: De acordo com amostra considerada não foram encontrados resultados referentes à utilização atual de SIS do tipo PEP, dado esse confirmado pela Controladoria Geral da União (CGU), informando que o Ministério da Saúde não fornece solução e suporte para soluções em software para utilização de PEP em hospitais públicos do Brasil, sendo esta a principal lacuna destacada neste estudo

Predição temporal de parâmetros da qualidade da água usando redes neurais profundas / Temporal prediction of water quality parameters using deep neural networks

The quality of the water is directly related to its level of pollution, and for that, monitoring is necessary to identify the physical, chemical and biological characteristics, considering the current legislation. This paper presents a comparison between the Long-Short Term Memory (LSTM) and Perceptron Multilayer (MLP) neural network models to predict pH, OD, BOD, Phosphorus, Turbidity, Temperature, Solid, and faecal coliforms of water quality. The error metrics MAPE, RMSE and MSE were used, when the neural networks are configured with 10, 25 and 50 neurons. In five water quality parameters, the LSTM network presented an average RMSE of 0.21, an average MSE of 0.11 and an average MAPE of 5.68. The MLP network showed an average RMSE of 0.21, an average MSE of 0.10 and an average MAPE of 5.55. The results of the experiments aim to contribute to the process of monitoring water quality and to help planning water management through the appropriate machine learning model for predicting parameters. 

AutoAssemblyD software para submissão e gerenciamento de montagem de genomas a partir de modelos XML

Technologies for second-generation sequencing provided a major breakthrough of the genome, making its use a landmark that has revolutionized biology. These platforms are characterized by a reduction in sequencing time, high data production and low cost per base sequenced, however, these devices produce data mostly consist of short readings which represents a major challenge for reconstruction of the genome due to this new feature readings of computational tools had to be developed to accomplish the task of assembling their example we Velvet, AllPaths, Abyss, SOAPdenovo2, Edena. However, most of these applications are executed through command lines extended and composed of several parameters must follow the standard syntax to use, because in case of errors in the syntax is the possibility of not obtaining the best result, with the aim of solve this problem we present the AutoAssemblyD that besides providing the use of these assemblers through a graphical interface also enables the management of these executions remotely.CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível SuperiorAs tecnologias de sequenciamento de segunda geração proporcionaram um grande avanço dos estudos genômicos, tornando sua utilização um marco que revolucionou a biologia. Estas plataformas são caracterizadas pela redução no tempo de sequenciamento, alta produção de dados e baixo custo por base sequenciada, contudo, estes equipamentos em sua maioria produzem dados compostos por leituras curtas o que representa um grande desafio para reconstrução do genoma, devido a essa nova característica das leituras ferramentas computacionais tiveram que ser desenvolvidas para realizar a tarefa de montagem exemplo delas temos Velvet, Allpaths, ABySS, SOAPdenovo2, Edena. No entanto, a maioria destes aplicativos são executados através de linhas de comandos extensas compostas por vários parâmetros e devem obedecer a uma sintaxe adequada a sua utilização, pois em caso de erros existe a possibilidade de não obtenção do melhor resultado, com o intuito de resolver este problema apresentamos o AutoAssemblyD, que além de proporcionar a utilização destes montadores através de uma interface gráfica também possibilita a gerência destas execuções de forma remota

ImproveAssembly - Tool for identifying new gene products and improving genome assembly.

The availability of biological information in public databases has increased exponentially. To ensure the accuracy of this information, researchers have adopted several methods and refinements to avoid the dissemination of incorrect information; for example, several automated tools are available for annotation processes. However, manual curation ensures and enriches biological information. Additionally, the genomic finishing process is complex, resulting in increased deposition of drafts genomes. This introduces bias in other omics analyses because incomplete genomic content is used. This is also observed for complete genomes. For example, genomes generated by reference assembly may not include new products in the new sequence or errors or bias can occur during the assembly process. Thus, we developed ImproveAssembly, a tool capable of identifying new products missing from genomic sequences, which can be used for complete and draft genomes. The identified products can improve the annotation of complete genomes and drafts while significantly reducing the bias when the information is used in other omics analyses

BADASS: BActeriocin-Diversity ASsessment Software

Abstract Background Bacteriocins are defined as thermolabile peptides produced by bacteria with biological activity against taxonomically related species. These antimicrobial peptides have a wide application including disease treatment, food conservation, and probiotics. However, even with a large industrial and biotechnological application potential, these peptides are still poorly studied and explored. BADASS is software with a user-friendly graphical interface applied to the search and analysis of bacteriocin diversity in whole-metagenome shotgun sequencing data. Results The search for bacteriocin sequences is performed with tools such as BLAST or DIAMOND using the BAGEL4 database as a reference. The putative bacteriocin sequences identified are used to determine the abundance and richness of the three classes of bacteriocins. Abundance is calculated by comparing the reads identified as bacteriocins to the reads identified as 16S rRNA gene using SILVA database as a reference. BADASS has a complete pipeline that starts with the quality assessment of the raw data. At the end of the analysis, BADASS generates several plots of richness and abundance automatically as well as tabular files containing information about the main bacteriocins detected. The user is able to change the main parameters of the analysis in the graphical interface. To demonstrate how the software works, we used four datasets from WMS studies using default parameters. Lantibiotics were the most abundant bacteriocins in the four datasets. This class of bacteriocin is commonly produced by Streptomyces sp. Conclusions With a user-friendly graphical interface and a complete pipeline, BADASS proved to be a powerful tool for prospecting bacteriocin sequences in Whole-Metagenome Shotgun Sequencing (WMS) data. This tool is publicly available at https://sourceforge.net/projects/badass/

Draft genome sequence of Psychrobacter sp. ENNN9_III, a strain isolated from water in a polluted temperate estuarine system (Ria de Aveiro, Portugal)

The genus Psychrobacter includes Gram-negative coccobacilli that are non-pigmented, oxidase-positive, non-motile, psychrophilic or psychrotolerant, and halotolerant. Psychrobacter strain ENNN9_III was isolated from water in a polluted temperate estuarine system, contaminated with hydrocarbons and heavy metals. The genome has a G + C content of 42.7%, 2618 open reading frames (ORFs), three copies of the rRNAs operon, and 29 tRNA genes. Twenty-five sequences related to the degradation of aromatic compounds were predicted, as well as numerous genes related to resistance to metals or metal(loid)s. The genome sequence of Psychrobacter strain ENNN9_III provides the groundwork for further elucidation of the mechanisms of metal resistance and aromatic compounds degradation. Future studies are needed to confirm the usefulness of this strain for bioremediation proposes

CODON-Software to manual curation of prokaryotic genomes.

Genome annotation conceptually consists of inferring and assigning biological information to gene products. Over the years, numerous pipelines and computational tools have been developed aiming to automate this task and assist researchers in gaining knowledge about target genes of study. However, even with these technological advances, manual annotation or manual curation is necessary, where the information attributed to the gene products is verified and enriched. Despite being called the gold standard process for depositing data in a biological database, the task of manual curation requires significant time and effort from researchers who sometimes have to parse through numerous products in various public databases. To assist with this problem, we present CODON, a tool for manual curation of genomic data, capable of performing the prediction and annotation process. This software makes use of a finite state machine in the prediction process and automatically annotates products based on information obtained from the Uniprot database. CODON is equipped with a simple and intuitive graphic interface that assists on manual curation, enabling the user to decide about the analysis based on information as to identity, length of the alignment, and name of the organism in which the product obtained a match. Further, visual analysis of all matches found in the database is possible, impacting significantly in the curation task considering that the user has at his disposal all the information available for a given product. An analysis performed on eleven organisms was used to test the efficiency of this tool by comparing the results of prediction and annotation through CODON to ones from the NCBI and RAST platforms