https://www.biolscigroup.us/journals/open-journal-of-bioinformatics-and-biostatistics A Peertechz Open Access Journal en-us 31 Dec, 2024 https://www.biolscigroup.us/articles/OJBB-8-114.php Back haulage or triangle routes are a suitable means of achieving a reduction in empty runs in timber transport. The calculation is done using linear programs. One problem with linear programs is the high complexity caused by the combinatorics involved in generating the routes. This can be reduced if the characteristics of back haulage or triangle routes are taken into account. The complexity then drops drastically and well-compatible linear programs are obtained. The methodology presented in this study was tested for the harvest sizes of the 2015 fiscal year of the Bavarian State Forest Enterprise. Pure back haulage routes lead to a reduction in empty runs of 17.2% and the combination of back haulage and triangle routes lead to a reduction of 20.2%. 13 Jul, 2023 https://www.biolscigroup.us/articles/OJBB-7-113.php Red seaweeds such as Kappaphycus alvarezii and Porphyra yezoensis have many applications, especially in the food industry, which suggests the need for knowing their potential allergenicity. In silico approaches can be used to determine if a protein is an existing allergen or has the ability to cross-react with one. In this study, 318 sequences for Kappaphycus alvarezii and 641 protein sequences for Porphyra yezoensis were screened for potential allergens using AlgPred 2.0 and AllergenOnline, followed by the FAO allergenicity test using Allermatch. Data from this were used to predict the B-cell epitopes using the IEDP prediction tool and T-cell epitopes using MHC2Pred and were modeled using SWISS-MODEL and PyMOL to highlight specific epitopes. These models were assessed for quality using Global Quality Model Estimate (GQME) scores, ERRAT scores, and VERIFY 3D. Results showed fourteen (14) potential red seaweed allergens, four (4) of which were found in Kappaphycus alvarezii and ten (10) in Porphyra yezoensis. Several proteins of red seaweeds shared structural similarities with species normally associated with food allergies, such as common hazel, Atlantic salmon, and shark catfish, as well as other types of allergens such as those in house-dust mites, that could potentially induce cross-reactivity. Additionally anticipated were specific B-cell and T-cell epitopes and their specific peptide sequences that were incorporated in the 3D models, which were created for further comparison with other molecular structures of recognized allergens. Almost all of the 3D models had a GQME score of above 0.7 and had a high ERRAT score for overall quality but some failed to pass the VERIFY 3D test. This study could serve as a preliminary yet robust approach to identifying allergenic proteins in red seaweed and narrowing down potential existing cross-reactive allergens from various species that could aid in future in vitro and in vivo allergenicity studies. 07 Sep, 2021 https://www.biolscigroup.us/articles/OJBB-5-111.php Mycobacterium is immovable induce aerobic, acid-fast gram-positive bacilli with high genomic content (59-66%). In the operon structure frequently establish for the genes of three molecular components: the ABC-binding protein, the membrane protein, and the substrate-binding protein, the rates of multidrug resistant and metal ions. The main objective of this study was to analyze the metal ions from five Mycobacterium species and to identify the metal transporters with “Genomic Island” associated features, in-silico analysis allowed identification of metal and drug transporters, phylogenetic analysis, genomic island path analysis, prediction of interacting metal ions, 3D structure, domain analysis and for the NiCoT metal transporter from Mycobacterium tuberculosis. These data are the first results of a big frame project that aims to accelerate the prioritizing of gene candidates that control element accumulation by taking advantage of high-throughput. The present in-silico study reveals the complete suite of NiCoT Metal Transporter in Mycobacterium tuberculosis H37Rv, which is involved in urease enzyme activity and biological function. The STRING analysis defines that the functional partners involved in transport of metal ions. While high expression yields of membrane proteins remain significant bottleneck for many proteins. 11 Aug, 2021 https://www.biolscigroup.us/articles/OJBB-5-110.php The colloidal complex of soils is the fine and supreme functional section of the organic and inorganic soil particles where most of the chemical properties take place. The inorganic or clay colloidal complex of soils occurs as too fine particles and organic colloidal complex happen in the form of humus particles. Soil colloidal fraction is the site of important processes in soil, governing ion exchange, nutrient availability and fixation, and soil physical properties. Based on the silicate and crystalline nature of the colloid mineral colloids are classified into three. These are crystalline layer silicate clays, noncrystalline layer silicate clays, and non-silicate clays. The organic colloidal complex in soils is mainly because of the existence of hummus. Shape, surface area, plasticity, cohesion, swelling, shrinkage, dispersion, and flocculation are the most important properties of soil colloids. 28 Jun, 2021 https://www.biolscigroup.us/articles/OJBB-5-109.php In this work, we used the quantum density theory (DFT), B3LYP / 6-311G (d, p) to establish a QSAR (Quantitative Structure Activity Relationships) model on a series of molecules derived from 2-thioarylalkyl-1H -Benzimidazole. This model is built with molecular descriptors and anthelmintic activities against the haemonchus contortus. The statistical indicators of this model are: the coefficient of determination R2, a standard deviation S, the Fisher coefficient F and the cross-validation coefficient Q2cv. The statistical parameters of the model are efficient. The quantum descriptors responsible for the anthelmintic activity of 2-thioarylalkyl-1H-Benzimidazole derivatives are the dipole moment (μ), the energy of the highest occupied orbital (EHOMO), the smallest negative charge of the molecule (q-). The acceptance criterion of Eriksson et al. used for the test series is verified. For the external validation, the values ​​of the ratio of theoretical activity and experimental activity tends to unity. 31 Dec, 2020 https://www.biolscigroup.us/articles/OJBB-4-108.php After the initial outbreak in Ethiopia, the dispersion of SARS-CoV-2 is elevated number of cases. Literally, reported results for confirmed cases peaked in August 2020 and declined after that time, as evidenced by the contestd responses that have invested in pandemic control in the country. ARIMA models are a most widely used approaches to time series forecasting and provide harmonizing approaches to the problem of forecasting. ARIMA models aim to describe autocorrelations in the data. Thus, in this study, the Autoregressive Integrated Moving Average (ARIMA) method is used to predict the number of new coronavirus cases. In short, Auto regression uses the dependent relationship between observation and lagged observations; Integrated using the difference in raw observations; and Moving Average relies on the dependency between observation and residual error. ARIMA (2, 2, 2) predicts the number of confirmed cases of COVID-19, based on the period between March 2020 and December 2020 at 95% confidence intervals. The result revealed that the maximum expected new case per day was 807 and the minimum forecast was 410 cases per day in the next two months. In addition, the total number of confirmed COVID-19 expected cases could reach about 160585 by end-February 2021. In general, if the government of Ethiopia stops controlling the COVID-19 mechanisms the pandemic may relapse severely and affect the country more. The study therefore proposed that the constructive stepladder incorporates control mechanisms. Thus, depending on the results of the report, all the organizations involved will establish policies. 17 Sep, 2020 https://www.biolscigroup.us/articles/OJBB-4-107.php This study uses an in silico approach in screening nascent allergens in GMO and conventionally-bred rice. The protein sequences analyzed were taken from published microarray data from GMO and conventionally-bred rice. To determine the proteins’ potential allergenicity, we used allergen databases and algorithms such as Allermatch and Algpred. Our analysis revealed the following putative allergenic proteins in GMO rice, namely: a cysteine proteinase precursor, a putative germin A, a glycosyl hydrolase, a subtilisin-like serine proteinase and an unknown protein. These genes are related to stress and defense response, metabolism, and moving, modifying, storing, and degradation of proteins. 31 Jul, 2020 https://www.biolscigroup.us/articles/OJBB-4-106.php MERS-CoV was emerged for the first time in KSA; 2012 followed by a lot of new registered cases in the Middle East, European, American and African countries. The goal of this paper is to make a comparison between the partial spike-glycoprotein reference gene (NC_019843.3; genome region: 23864-24909 with 1046bp) with similar Sudanese camel sequences; using the NCBI data base. Creations of phylogenetic tree for those who were selected as reference genes from Middle East countries (Qatar, UKE, and KSA), south East Asia and African countries (Ethiopia, Egypt, Nigeria, Burkina Faso) with Sudanese sequences using ViPR website was done. This study revealed that most of the Sudanese sequences descending from each other’s with a lot of mutations area which mainly concentrated at positions; 155, 156, 158, 242, 840, 876 at nucleotide levels and to explain these more in-depth studies are recommended. 19 Jun, 2020 https://www.biolscigroup.us/articles/OJBB-4-105.php The prerequirement of genetic engineering is to have knowledge about structure and function of transgene and its encoded protein. 27 Jun, 2017 https://www.biolscigroup.us/articles/OJBB-1-103.php Biological sciences have been for so long dominated by observational approaches as shown by the scarcity of studies trying to infer causality from association, starting from the historical and very instructive studies of Pierre Louis (1835) on the efficacy of the standard treatments for pneumonia and John Snow (1855) on the causal relationship between cholera and water contamination [1]. 24 Mar, 2017 https://www.biolscigroup.us/articles/OJBB-1-102.php Background: Computational analyses have shown great potentials for providing tools for the rapid detection and identifi cation of fungi for medical, scientifi c and commercial purposes. Various bioinformatics tools have been developed for fi nding the specifi c regions within the ribosomal RNA (rRNA) gene complex. Candida is a genus of yeast that includes about 150 different species and is the most common cause of human ocular infections. In the present study, rapid detection method of Candida, based on specifi c regions (18S, 5.8S and 28S) of ribosomal RNA (rRNA) genes of eight (8) species e.g. C. albicans, C. krusei, C. parapsilosis, C. glabrata, C. guilliermondii, C. kefyr, C. lusitaniae and C. tropicalis has been developed. Rapid diagnosis and early identifi cation of causative agent through computational based methods with high accuracy will result in effective treatment. 27 Jan, 2017 https://www.biolscigroup.us/articles/OJBB-1-101.php Objectives: The aim of study was to evaluate the Compliance to the Government Act on Cigarettes and Other Tobacco Products (COTPA Act 2003) Section 6 that protects the exposure of under 18 children to tobacco products and to identify areas of violations, near Educational Institutions (EIs) in Noida.