Categories
Tag: COG
Significance of Dashes (-) as COG category in EGGNOG-Mapper
Significance of Dashes (-) as COG category in EGGNOG-Mapper 0 Seeking clarification on COG categories analysed via eggnog-mapper. while analyzing the output derived from EGGNOG-mapper, I noticed dashes (“-“) in some COG categories, and I’m curious if this indicates non-applicability or undefined functional assignments for associated proteins. Could someone confirm…
A Database of RNA Modifications
Modomics – A Database of RNA Modifications RsmA from Thermus thermophilus – protein summary. ID Card: Full name: Ribosomal RNA small subunit methyltransferase A Synonym: KsgA, TTHA0083 GI: 55980052 COG: COG0030 UniProt: Q5SM60 Structures: | 3FUT | 3FUU | 3FUW | 3FUV | 3FUX | Enzyme type: methyltransferase Position of…
Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis
Whole genome sequencing and analysis To understand the mechanisms underlying the biological control capability of bacterial pathogens, the complete genome of MEP218 was sequenced, assembled, and deposited in the GenBank database under the accession number CP042864.2. The genome of MEP218 consists of a single circular chromosome of 3,944,892 bp with a…
Panel-based RNA fusion sequencing improves diagnostics of pediatric acute myeloid leukemia
Rasche M, Zimmermann M, Borschel L, Bourquin J, Dworzak M, Klingebiel T, et al. Successes and challenges in the treatment of pediatric acute myeloid leukemia: a retrospective analysis of the AML-BFM trials from 1987 to 2012. Leukemia. 2018;32:2167–77. Article PubMed PubMed Central Google Scholar Manola KN. Cytogenetics of pediatric acute…
Resin acids play key roles in shaping microbial communities during degradation of spruce bark
Bark preparation Spruce bark was obtained from the Iggesund pulp and paper mill (Iggesund, Holmen AB, Sweden), from a bark pile resulting from stripping of spruce logs at the mill after harvest, with the average age of trees at harvest being ~70 years. The bark was left to dry at…
Phase 3 Findings Demonstrate Impacts of NE3017 in Alzheimer Cognition, Function
Newly announced topline data from a phase 3 study (NCT04669028) of BioVie’s Alzheimer agent NE3107 showed beneficial treatment effects over placebo that were potentially equal to or greater than data reported from previously approved antiamyloid therapies. In addition, patients on the permeable anti-inflammatory insulin sensitizer saw an average of more…
Data Science Major – Bioinformatics Track
It’s not just about the numbers. Data science, the study of how to extract meaning from data, is a growing field that can provide students with exciting and rewarding career paths, with opportunities for advanced study in various disciplines. Data scientists can help address the pressing concerns of modern society,…
Survey of the infant male urobiome and genomic analysis of Actinotignum spp.
Wolfe, A. J. et al. Evidence of uncultivated bacteria in the adult female bladder. J. Clin. Microbiol. 50, 1376–1383 (2012). Article PubMed PubMed Central Google Scholar Hilt, E. E. et al. Urine is not sterile: Use of enhanced urine culture techniques to detect resident bacterial flora in the adult female…
NE3107 does well in Alzheimer’s trial, despite protocol issues
NE3107, BioVie Pharma’s experimental oral therapy, was superior to a placebo at improving performance of adults with mild-to-moderate Alzheimer’s disease on all cognitive and functional assessments of a Phase 3 clinical trial, top-line efficacy data shows. However, these differences failed to reach statistical significance due to a loss of the…
BioVie Announces Efficacy Data from Phase 3 Trial of
Positive Trending Data from 57 Per-Protocol Patients Suggest NE3107 is Biologically Active and May Have Impact on Cognitive, Functional, and Biomarker Endpoints Sponsor Identified Issues Relating to Significant GCP Violations and Protocol Deviations, Which Allowed for Data from Only a Subset of Enrolled Patients to be Included in the Efficacy Analysis;…
How can I amend the output of a DIAMOND python script?
Hello, please help a struggling wet-lab biologist. I am trying to identify Cluster of Orthologous Groups (COG) categories for a list of gene sequences. I configured a COG database and used DIAMOND to blast query sequences against this database. This provides a results.cog file that in my case is formatted…
Whole genome sequencing provides evidence for Bacillus velezensis SH-1471 as a beneficial rhizosphere bacterium in plants
Inhibition effect of strain SH-1471 on plant pathogenic fungi The results of the plate confrontation experiment showed that B. velezensis SH-1471 had good inhibitory effects on various pathogenic microorganisms (Fig. 1). Specifically, our experiment showed that its inhibition rates on Sclerotinia scrotiorum, Phoma mateuciicola, and Fusarium oxysporum were 93.5%, 90.3%, and…
normalize not left-normalizing?
I’m running plink2 to convert a vcf to a pgen with pseudobiallelic variants. Calling –normalize does not seem to left-normalize as I would expect, at least when I look at the .pvar. Log PLINK v2.00a6LM AVX2 Intel (21 Nov 2023) www.cog-genomics.org/plink/2.0/(C) 2005-2023 Shaun Purcell, Christopher Chang …
Fermentation | Free Full-Text | Whole-Genome Sequencing of Lactiplantibacillus plantarum YY-112 and Investigation of Its Immune-Modulating Abilities In Vivo
Author Contributions Conceptualization, Y.Y. and Y.G.; Data curation, M.L. and W.Z.; Formal analysis, M.L., W.Z., W.T. and J.L.; Funding acquisition, Y.Y. and Y.G.; Investigation, J.X., Y.Y. and Y.G.; Methodology, M.L., J.L. and Y.Y.; Project administration, Y.Y.; Resources, J.X., Y.Y. and Y.G.; Software, M.L., W.Z. and W.T.; Supervision, J.X., Y.Y. and…
BioVie: Cautiously Optimistic Ahead Of Phase 3 Alzheimer’s Data Unblinding (NASDAQ:BIVI)
BlackJack3D Intro Neurodegenerative disease-focused BioVie (NASDAQ:BIVI) recently presented a set of blinded data which, if taken at face value, suggest that its lead asset NE3107 may have robust (and potentially unprecedented) cognitive and biomarker efficacy in Alzheimer’s disease. On October 25th, the company presented blinded data from its Phase 3…
Taxonomic and environmental distribution of bacterial amino acid auxotrophies
Tripp, H. J. et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452, 741–744 (2008). Article ADS CAS PubMed Google Scholar Yu, X. J., Walker, D. H., Liu, Y. & Zhang, L. Amino acid biosynthesis deficiency in bacteria associated with human and animal hosts. Infect. Genet. Evol….
Taxonomic identification and temperature stress tolerance mechanisms of Aequorivita marisscotiae sp. nov
Zain ul Arifeen, M., Ma, Y.-N., Xue, Y.-R. & Liu, C.-H. Deep-sea fungi could be the new arsenal for bioactive molecules. Mar. Drugs 18, 9 (2020). Article Google Scholar Martínez-Espinosa, R. M. Microorganisms and their metabolic capabilities in the context of the biogeochemical nitrogen cycle at extreme environments. Int. J….
Gotta Get Rid of It All: Total Plaque Clearance Key for Clinical Benefit
18 Nov 2023 As researchers parse what makes amyloid immunotherapy work, one answer keeps bubbling up: Take out all plaque quickly, so that clinical benefits have time to show up. At last month’s Clinical Trials on Alzheimer’s Disease conference, held October 24 to 27 in Boston and online, several talks…
Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient
Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA. 103, 626–631 (2006). Article ADS CAS PubMed PubMed Central Google Scholar Gao, C. & Guo, L. Progress on microbial species diversity, community assembly and functional traits. Biodivers. Sci. 30, 22429 (2022)….
BioVie: Upcoming Phase 3 Readout In Alzheimer’s May Create Significant Value (NASDAQ:BIVI)
nantakorn jeenpueng Thesis BioVie (NASDAQ:BIVI), currently valued by the market at about $120 million, is about to report topline data from a Phase 3 study in Alzheimer’s disease [AD] between Thanksgiving and early December. In my previous coverage, I had argued that the baseline data in about 75% of patients…
Plink2 PCA approx memory allocation
This is great, thank you! Will this information be included in the PLINK2 documentation? The successful run we had included the log below. In the “Projecting random vectors” line, 21 steps are described, rather than the number 20 of requested principal components. I assume this is part of how the…
A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources
40,039 MAGs reconstructed from large-scale genome-resolved metagenomics To reconstruct previously unexplored bacterial and archaeal genomes, we performed a large-scale single-sample metagenomic assembly on 3304 soil metagenomes across the globe (Fig. 1a), including 363 metagenomes from the in-house dataset and 2941 from publicly available metagenomes. The soil samples were mainly collected from…
Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics
Albone, E. S. Mammalian semiochemistry. The investigation of chemical signals between mammals. 2–5 (1984). Wyatt, T. D. Pheromones and Animal Behaviour: Communication by Smell and Taste (Cambridge University Press, 2003). Book Google Scholar Doty, R. L. Odor-guided behavior in mammals. Experientia 42, 257–271 (1986). Article CAS PubMed Google Scholar Brennan,…
PLINK 1.9 meta-analysis
I’m trying to meta-analyze together some PLINK2 (“–glm omit-ref hide-covar cols=+a1freq,+beta”) outputs. I think I’m having trouble understanding the syntax requirement for the PLINK 1.9’s –meta-analysis feature. I interpreted the doc as indicating that adding ‘logscale’ after the filenames would cause it to look for ‘BETA’ in the input. PLINK…
‘PC1’ entry on line 8297 of is categorical
> str(pheno_cov$PC1) num [1:10691] -0.0016 -0.001615 -0.001843 -0.001882 -0.000693 … PLINK v2.00a3.6LM AVX2 Intel (14 Aug 2022) www.cog-genomics.org/plink/2.0/(C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3Logging to ./res/test_plink2.log.Options in effect: –bfile updateID_geno0.02_maf0.005 –ci 0.95 –covar ./pheno_cov/pheno_cov.txt –covar-name Sex_Code,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10 –covar-variance-standardize –glm hide-covar omit-ref –memory 200000 –out…
Plink Error
Plink Error 1 Hi I am trying to convert ped file for hapmap3 I downloaded here ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2009-01_phaseIII/plink_format/ and unzipped with binzip2 but I am getting the following error when running this command PLINK v1.90b5.2 64-bit (9 Jan 2018) www.cog-genomics.org/plink/1.9/ (C) 2005-2018 Shaun Purcell, Christopher Chang GNU General Public License v3…
No valid entries in –score file
PLINK Error: No valid entries in –score file 0 Hi, I ran this command on plink1.9 to calculate the poligenic score. plink –vcf sample –score output.txt 1 2 3 –out poligenic_results – output.txt: ID ALT UKB-b-15541 rs10399793 C 0.000345793 rs2462492 T -0.00027716 – sample.vcf: #CHROM POS ID REF ALT QUAL…
Longtime UVM professor honored for work with Vermont endangered species
Kilpatrick’s deer mouse. Wikimedia Commons When Bill Kilpatrick completed his doctorate in zoology back in 1973, the Texan was not at all interested in finding a job east of the Mississippi. As luck would have it, he landed a job as a professor at the University of Vermont the following…
No samples in .vcf file.
I am trying to convert my vcf file into a BED format file. When I use this command: plink –vcf merge.bacteria.vcf.gz –make-bed –out merge.bacteria.vcf.bed I get the following error stating: PLINK v1.90b6.21 64-bit (19 Oct 2020) www.cog-genomics.org/plink/1.9/(C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License…
Plink2 error
I downloaded data from 1000 genomes website. MacBook-Air-4:plink_mac mac$ ./plink –vcf ALL.chr1.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf –make-bed –out char1 PLINK v1.90p 64-bit (13 Feb 2023) www.cog-genomics.org/plink/1.9/ (C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to char1.log. Options in effect: –make-bed –out char1…
NGS Training | Top NGS Courses | Online Training | RNASeq | Genome Variant Detection
NGS Training Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. NGS methods are highly parallelized enabling to sequence thousands to millions of molecules simultaneously. This technology results into huge amount of data, which…
Troubleshooting multallelic variant merging issue
Hello, I want to recode the IIDs of imputed data .bgen files into two different filesets, and merge these (working on eye-level analyses with Regenie). As I’m only interested in dosages, I’ve converted these to .pgen using PLINK2 (ref-first as UK Biobank): plink2 –bgen data.bgen ref-first –sample data.sample –update-ids recoded_ids_a.txt –make-pgen…
Transcriptome analysis of Haemaphysalis flava female using Illumina HiSeq 4000 sequencing: de novo assembly, functional annotation and discovery of SSR markers | Parasites & Vectors
Machado-Ferreira E, Vizzoni VF, Balsemao-Pires E, Moerbeck L, Gazeta GS, Piesman J, et al. Coxiella symbionts are widespread into hard ticks. Parasitol Res. 2016;115:4691–9. doi.org/10.1007/s00436-016-5230-z. Article PubMed Google Scholar Jung M, Kho JW, Lee WG, Roh JY, Lee DH. Seasonal occurrence of Haemaphysalis longicornis (Acari: Ixodidae) and Haemaphysalis flava, vectors…
Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space
Viromics datasets represent the sequence space of protected extracellular DNA (peDNA) The majority of samples prepared for “viromics” include GTAs and EVs, in addition to virus particles. All three entities are small protein- and/or lipid-containing particles that can enclose cellular DNA [3] or were found to bind cellular DNA on…
Widespread occurrence of chitinase-encoding genes suggests the Endozoicomonadaceae family as a key player in chitin processing in the marine benthos
Genes coding for endo-chitinases (EC 3.2.1.14), the enzymes that cleave chitin polymers into oligomers [16], were found on 32 of 42 Endozoicomonadaceae genomes (Fig. 1 and Table S1), including representatives of all formally described genera and all Candidatus Gorgonimonas MAGs. Several genomes harbored more than one endo-chitinase encoding gene, resulting in…
Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples
Tuganbaev, T. et al. Diet diurnally regulates small intestinal microbiome-epithelial-immune homeostasis and enteritis. Cell 182, 1441–1459 (2020). Article CAS PubMed Google Scholar Dejea, C. M. et al. Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria. Science 359, 592–597 (2018). Article CAS PubMed PubMed Central Google Scholar Bullman,…
Line 15522 of data/Pheno_KFs1.txt has fewer tokens than expected in GWAS analysis
I’m performing GWAS using UKB imputed genetic data below. However, I got the error as follows. plink2 –bfile data_TL –glm hide-covar –pheno data/Pheno_KFs1.txt –pheno-name LogBUN_mg_dl –covar data/Covariatesdata.txt –covar-name PC{1..10}, Age, Tuoi, Sex –extract TL_snplist_All.txt –out output/GWAS_BUN.cvrtPLINK v2.00a6LM 64-bit Intel (27 Sep 2023) www.cog-genomics.org/plink/2.0/(C) 2005-2023 Shaun Purcell, Christopher Chang…
Genotyping, sequencing and analysis of 140,000 adults from Mexico City
Recruitment of study participants The MCPS was established in the late 1990s following discussions between Mexican scientists at the National Autonomous University of Mexico (UNAM) and British scientists at the University of Oxford about how best to measure the changing health effects of tobacco in Mexico. These discussions evolved into…
Cassava Sciences: Unconvincing Open Label Studies, Upcoming Phase 3, Risky AD Bet (SAVA)
Naeblys The Alzheimer’s Disease (“AD”) space is a very difficult and volatile space right now. Here, you will see a large number of sympathetic volatility in stock prices. So, if one company comes out with positive data, other AD companies go up along with it. If another company has a…
Co-op students help feed the world at Waterloo-based startup Ceragen | HIRE Waterloo
By: Isabella Deak (she/her) A growing biotechnology startup, Ceragen, hires Waterloo co-op students to help meet its goal: feed the world. The company develops novel probiotics for the hydroponic greenhouse industry to increase its crop yields in the Tannery in downtown Kitchener. Today, Ceragen is seeing yield increases of up…
Virulence Characteristics of Salmonella Enteritidis
Introduction As an important zoonosis pathogen, Salmonella is widely distributed in nature and one of the four major pathogens causing global diarrhea diseases.1 Salmonella has six subspecies and 2659 serotypes, among which Salmonella Enteritidis (S. Enteritidis) are the most common serotypes causing Salmonella outbreaks.1 S. Enteritidis has a wide variety…
Epidemiology and analysis of SARS-CoV-2 Omicron subvariants BA.1 and 2 in Taiwan
Prevalence of Omicron subvariants between December 2021 and January 2023 in Taiwan BA.1 and BA.2 and their sublineages entered Taiwan in December 2021 and January 2022, respectively (Supplementary Table S1 and Fig. 1). These two Omicron lineages did not cause COVID-19 outbreaks until March and April 2022 (Supplementary Table S1 and…
Assistant Professor in Forensic Sciences job with NORTHUMBRIA UNIVERSITY
ABOUT THE ROLE Working within the Department of Applied Sciences, this role involves both teaching and research. The successful candidate will be part of a multidisciplinary team that teaches undergraduate and postgraduate forensic science students, on programmes accredited by the Chartered Society of Forensic Sciences. This post will involve designing,…
Issue with Numerical Covariate * Covariate Interaction in Association Analysis
I tried to perform a covariate-covariate interaction analysis using numerical covariates of interest, namely activity_data and age. However, I encountered an error message stating that the number of samples was equal to or less than the number of predictor columns for the specified phenotype. Just to make sure I run…
BioVie Announces Completion of Last Patient Treatment Visit in Phase 3 Trial of NE3107 in Mild to Moderate Alzheimer’s Disease
Expects to announce topline data expected in the November/December timeframe. Enrolled patients had underlying medical conditions that are known risk factors for dementia that NE3107 has the potential to improve. /EIN News/ — CARSON CITY, Nev., Sept. 26, 2023 (GLOBE NEWSWIRE) — BioVie Inc., (NASDAQ: BIVI) (“BioVie” or the “Company”)…
BioVie Inc Concludes Phase 3 Clinical Trial of NE3107 in Alzheimers Disease Patients
On September 26, 2023, BioVie Inc. successfully concluded the final patient treatment visit for its groundbreaking Phase 3 clinical trial of NE3107 in individuals suffering from mild to moderate Alzheimer’s Disease. This comprehensive study, encompassing 316 to 400 patients, aimed to evaluate the efficacy of NE3107 in improving cognitive function…
BioVie to announce topline data from Phase 3 Alzheimer’s Disease trial by year-end
BioVie Inc (NASDAQ:BIVI) said the last patient has completed their final visit at week 30 in their Phase 3 study of investigational therapy NE3107 in patients with mild to moderate Alzheimer’s Disease (AD), and it expects to announce topline data from the trial in November or December. BioVie’s shares moved higher…
A metagenomic catalog for exploring the plastizymes landscape covering taxa, genes, and proteins
Construction of integrated PCEG and PCEP To the best of our knowledge, the present study is the first to develop a comprehensive catalog of plastic-contaminated soils using an integrated bioinformatic workflow. Five datasets were used to produce 53,300,583 unique genes and proteins. Quality control of reads, trimming, assembly, and binning…
Lecturer in Forensic Sciences job with NORTHUMBRIA UNIVERSITY
ABOUT THE ROLE Working as part of multi-disciplinary teams, you will be responsible for contributing to an exceptional student experience through the delivery of teaching, research, knowledge exchange and business and enterprise engagement activity. Colleagues appointed into our Lecturer grade are usually early career academics who are supported through their…
Genetic distance in cM from VCF of non-reference species to run Beagle
I’m working with a resequenced genome of a non-reference species. The VCF contains ~7 mln of SNPs, all with their relative position on their own chromosome. I have a 10.01 % of missing data, so I need to impute these NA. I eventually settled for Beagle v5 as a tool,…
Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli
PPTP-seq development and validation PPTP-seq uses plasmid to integrate each CRISPRi-based TF perturbation and each promoter activity reporter into one construct. Each plasmid contains a CRISPRi cassette that constitutively expresses a single guide RNA (sgRNA) to repress a specific TF in the genome19 and a promoter-reporter cassette to measure the…
Invalid .bed file size (expected 9996779 bytes)
Hello Christopher, We have data in PGEN format, and as part of our workflow, we initially created temporary PSAM, PVAR, and PGEN files using the following command:./plink2 –bgen data.bgen ref-first –sample data.sample –set-missing-var-ids @:#:’\$r’:’\$a’ –new-id-max-allele-len 99 truncate –make-pgen –out data.intermediate 2. Following this step, we convert these temporary files to…
One high quality genome and two transcriptome datasets for new species of Mantamonas, a deep-branching eukaryote clade
Isolation and microscopy of Mantamonas sphyraenae sp. nov Mantamonas sphyraenae SRT-306 was collected on 26 Sep. 2013 from the surface of a barracuda caught in a lagoon on Iriomote Island, Taketomi, Okinawa Prefecture, Japan (24° 23′ 36.762″ N, 123° 45′ 22.572″ E). It was isolated manually from the rough sample…
SC2EGSet: StarCraft II Esport Replay and Game-state Dataset
Reitman, J. G., Anderson-Coto, M. J., Wu, M., Lee, J. S. & Steinkuehler, C. Esports Research: A Literature Review. Games and Culture 15, 32–50, doi.org/10.1177/1555412019840892 (2020). Article Google Scholar Chiu, W., Fan, T. C. M., Nam, S.-B. & Sun, P.-H. Knowledge Mapping and Sustainable Development of eSports Research: A Bibliometric…
BioVie: Well-Powered Phase 3 Trial In Alzheimer’s Could Greatly Benefit Investors
KanawatTH/iStock via Getty Images Thesis It has been about five months since I last covered BioVie. This should be the last article on the company prior to topline data from its Phase 3 trial in Alzheimer’s disease [AD] in October-November 2023. I believe there are good chances of success for…
Genome-wide analysis identifies novel loci influencing plasma apolipoprotein E concentration and Alzheimer’s disease risk
The details of study participants, plasma ApoE measurement, genotyping and imputation, statistical analyses, and functional annotations are given in Online Methods. Association of plasma ApoE concentration with incident dementia and cognition function Whole plasma ApoE concentration at baseline was determined in 3031 participants, of which 2893 were European Americans (EAs),…
Error page | Dice.com
WHAT ARE COOKIES? A cookie is a small file of letters and numbers that we store on your browser or the hard drive of your computer if you agree. Cookies contain information that is transferred to your computer’s hard drive. WHAT TYPES OF COOKIES DO WE USE? We use two…
Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland
Growth conditions and identification The growth of the strain W-6 was measured at different temperatures of 4, 10, 15, 20, 25, 30, and 37 °C. It can be seen that strain W-6 could grow at the range from 4 to 30 °C with the optimal growth temperature 15 °C. Then, the growth curve of…
Science: Metagenome sequencing reveals pathogen-mediated plant endophytes
Yi Gene|Science: Metagenome sequencing reveals pathogenic bacteria-mediated activation of plant endophyte disease-suppressive function Using metagenomics techniques of plant endophytes, researchers such as Carrión of the Netherlands Institute for Ecology have shown that certain “resident” bacteria can protect plant roots from fungal infection. It is revealed that microorganisms living inside plant…
Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer
Sample collection Previously, we collected nasal samples from WTD in northeastern Ohio focusing on metropolitan area parks11. In the present study, we expanded geographical study area by approximately 1000-fold to target the entire state of Ohio. We collected 1522 nasal swabs from WTD across 83 of Ohio’s 88 counties from…
A versatile, fast and unbiased method for estimation of gene-by-environment interaction effects on biobank-scale datasets
UK Biobank The UK Biobank is a large population-based study which includes over 500,000 participants living in the United Kingdom41,42 (www.ukbiobank.ac.uk/). Men and women aged 40–69 years were recruited between 2006 and 2010, and extensive phenotypic and genotypic data were collected. Quality control of genotype data was applied for individual…
Microorganisms | Free Full-Text | Genome-Wide and 16S rRNA Sequencing-Based Analysis on the Health Effects of Lacticaseibacillus paracasei XLK401 on Chicks
1. Introduction Since 2006, the European Union has prohibited the use of antibiotics in animal feed to boost growth [1]. This ban has resulted in a significant rise in disease outbreaks in broiler farming [2]. Therefore, there is an urgent need to find effective antibiotic alternatives for use in the…
reading pgen file into R
reading pgen file into R 1 Hi , i downloaded file form here : www.cog-genomics.org/plink/2.0/resources#phase3_1kg the hgdp_chr4.pgen.zst file I decompressen it to chr4.pfen file but Im havung trouble reading it into R would be happy for your help , tried to make it a bed file but it didnt help…
Answer: simulation
For example: You can use more complete genotype data from 1000 Genome. [https://www.cog-genomics.org/plink/1.9/resources][1] If you want more SNPs, you can impute them in `Michigan Imputation` or `TOPMed Imputation` Servers. [https://imputationserver.sph.umich.edu/index.html#!][2] [https://imputation.biodatacatalyst.nhlbi.nih.gov/#!][3] [1]: www.cog-genomics.org/plink/1.9/resources [2]: imputationserver.sph.umich.edu/index.html#! [3]: imputation.biodatacatalyst.nhlbi.nih.gov/#! Read more here: Source link
EggNOG mapper annotation results
I am new with Bioinformatics, I used eggnog to annotate a group of protein sequences The results obtained with eggnog are not very well explained, how do you interpret these results? Query | seed_ortholog | evalue | score | eggNOG_OGs | max_annot_lvl | COG_category | Description | Preferred_name | GOs…
Potential pathogenicity of Non-O1, Non-O139 V. cholerae
Introduction Vibrio cholerae is a Gram-negative bacterium that can be classified into different serotypes based on the O surface antigen, with O1 and O139 being responsible for causing cholera in humans. Cholera is a highly infectious and severe diarrheal disease that is prevalent worldwide, particularly in Africa, South Asia, and…
Whole genome sequencing and the lignocellulose degradation potential of Bacillus subtilis RLI2019 isolated from the intestine of termites | Biotechnology for Biofuels and Bioproducts
Screening and molecular identification of dominant cellulolytic bacteria Uniform screening procedures were performed to obtain the dominant cellulase-producing strain. Congo red plate staining reflected that clear hydrolysis circles were observed around Isolate C1 to C10, which indicated all strains could degrade CMC-Na. The qualitative assay for CMC-Na hydrolysis showed that…
Comparative genomics unveils extensive genomic variation between populations of Listeria species in natural and food-associated environments
Core genomes of Listeria species strongly differ between natural and food-associated environments and can accurately predict isolation sources at a lineage level To assess the relationship between the core genome of L. monocytogenes (which entails genomes of all three L. monocytogenes lineages identified in this study – lineage I, II,…
BioVie Pharma; Bullish Long-Term But Bearish On Upcoming Phase 3 Readout (NASDAQ:BIVI)
M-A-U/iStock via Getty Images Overview of the thesis BioVie Pharma (NASDAQ:BIVI) is developing NE3107 for Alzheimer’s Disease (AD) and Parkinson’s Disease (PD) and BIV201 for ascites (see pipeline in image below). All indications are phase-3-ready following promising results in phase 2 studies. BIVI estimates total peak sales potential of $34.6B…
Multiple record GenBank files
Multiple record GenBank files 0 Hello.The GenBank file I have includes multiple records, so generating ptt and rnt files (with gbkToPttAndRnt.py) resulted in multiple rnt and multiple ptt files – one for each record in the GenBank file. As instructed in the EDGE-pro manual, I merged the files.Trying to use…
Metagenomic analysis of soybean endosphere microbiome to reveal signatures of microbes for health and disease | Journal of Genetic Engineering and Biotechnology
Sequencing quality analysis To process the metagenome data analysis, dataset quality analysis was performed using the FastQC program. The FastQC program provides a QC report on spot problems that originate either in the sequencer or in the starting library material. Many modules were used to evaluate the raw data, and…
Comparative analysis of carbapenem-resistant K. pneumoniae
Introduction The worldwide spread of Klebsiella pneumoniae is a major global public health threat.1,2 K. pneumoniae is an opportunistic pathogen that colonizes the human gut and respiratory tract and possibly causes infection in immunocompromised hosts. Gut colonized K. pneumoniae is one of the important pathogens causing nosocomial infections, although the…
Evolutionary genomics of camouflage innovation in the orchid mantis
Sample collection Captive breeding individuals of H. coronatus (Mantodea, Hymenopodidae) hatched from the same ootheca that was collected from the Xishuangbanna rainforest, Yunnan Province, China in 2018. Individuals of D. lobata (Mantodea, Deroplatyidae) were collected from a captive breeding center in Beijing, China in 2018. All individuals were housed in semitransparent…
Apply Plink2 Score – Error Invalid chromosome code
I am trying to run a calculator tool for polygenic scores called pgsc_calc (The Polygenic Score Catalog Calculator pipeline) that runs with nextflow and docker in linux, with my own VCF file. Its failing step 8: process > PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:PLINK2_SCORE **ERROR ~ Error executing process > ‘PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:PLINK2_SCORE (NG13RY1WV.vcf.gz chromosome ALL effect…
filenameXYZ.bim could not be scanned twice, plink2
Hi Chris, I am using PLINK2 to merge heavy files (binary filesets) and then exporting them into bgen format. One of the file caused problem, if i remove that file – merging works. I tried to investigate whether it is problem with that specific input fileset, but if i only attempt…
A new era of pathogen surveillance using genomic sequencing
Image © JuSun | iStock We spoke to Dr Joanne Hackett, Former Chief Commercial Officer of Genomics England and Regional Board Member of Movement Health 2030, about how genomic sequencing supports preparedness and response to public health threats Genomic sequencing is a method scientists use to decipher the genetic material…
Generative AI applications in Health and Life Sciences and available Open Source AI tools. | by NEERAJ SHRIVASTAVA | Jul, 2023
Generative AI refers to a type of artificial intelligence that is capable of creating new content or data autonomously, often by mimicking or learning from existing data. Generative models are trained on large datasets and learn to understand patterns, structures, and relationships within the data. Once trained, these models can…
Cassava Science positive data continues to derisk ongoing phase 3 trials (NASDAQ:SAVA)
adamkaz/E+ via Getty Images I once again give Cassava Sciences (NASDAQ:SAVA) a strong buy rating, and as I have previously stated, I think Cassava Sciences is the best risk to reward on the market. I have been covering this stock for three years and have been very bullish on it…
Leqembi Granted Traditional Approval for Alzheimer Disease
The Food and Drug Administration (FDA) has granted traditional approval to Leqembi® (lecanemab-irmb) for the treatment of Alzheimer disease (AD) based on the clinical benefit established in a confirmatory trial. Leqembi is a humanized immunoglobulin gamma 1 (IgG1) monoclonal antibody directed against aggregated soluble and insoluble forms of amyloid beta….
First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome [PeerJ]
Introduction Vultures are obligate scavengers, birds of prey that provide several ecological services such as nutrient recycling or avoiding soil contamination by carcass feeding, which help to reduce the spread of diseases in their habitats (Ogada, Keesing & Virani, 2012; Chung et al., 2015; Buechley & Şekercioğlu, 2016). Vultures are…
Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains
Moya-Beltrán, A. et al. Genomic evolution of the class Acidithiobacillia: Deep-branching Proteobacteria living in extreme acidic conditions. ISME J. 15, 3221–3238 (2021). Article PubMed PubMed Central Google Scholar Nuñez, H. et al. Molecular systematics of the genus Acidithiobacillus: Insights into the phylogenetic structure and diversification of the taxon. Front. Microbiol….
PLINK1.9 check sex problem
PLINK1.9 check sex problem 0 Hello! I use plink1.9 with –check-sex option to check sex in data with only one sample. I use –read-freq with a file contained frequencies of variants from chrX of 1000G (obtained by –freq). My problem is that for all samples I have F=-1 and SNPSEX=2….
Prescription digital therapeutics are key to pharma’s future
Five years from now, when patients walk into a doctor’s office presenting symptoms of almost any condition you can envision — whether migraine, multiple sclerosis, or obesity — their physician will offer a new kind of treatment plan that involves both pharmaceutical-based medication and a prescription digital therapeutic. Accessible through…
Problem creating .bed files with plink
Problem creating .bed files with plink 0 Hello everyone, I’m having trouble creating a bed file with plink. Here is what my .ped file looks like: # Stacks v2.61; PLINK v1.07; July 02, 2023 Fos_ext XY1 0 0 0 0 0 0 0 0 0 0 0 0 0 0…
bgen, missing-code, and error in temporary.psam
Hello! I am trying to rerun (update) my analyses after reviewer responses. It has been a few years since I had to touch these files/code and I am running into problems that I did not have back in 2018 with the bgen files from ALSPAC. Specifically, that the temporary.psam file…
Ubuntu Manpage: Bio::Tools::Run::StandAloneNCBIBlast – Object for the local execution of the NCBI BLAST
Provided by: libbio-perl-run-perl_1.7.3-8_all NAME Bio::Tools::Run::StandAloneNCBIBlast – Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast. SYNOPSIS # Do not use directly; see Bio::Tools::Run::StandAloneBlast DESCRIPTION See Bio::Tools::Run::StandAloneBlast FEEDBACK Mailing Lists User feedback is an integral part of the evolution of…
Multivariate genetic analysis of personality and cognitive traits reveals abundant pleiotropy
Walhovd, K. B. et al. Neurodevelopmental origins of lifespan changes in brain and cognition. Proc. Natl Acad. Sci. USA 113, 9357–9362 (2016). Article CAS PubMed PubMed Central Google Scholar Damian, R. I., Spengler, M., Sutu, A. & Roberts, B. W. Sixteen going on sixty-six: a longitudinal study of personality stability…
Complexity is a barrier to horizontal gene transfer, shows new study
Tests of the balance and connectivity hypotheses. Plots show the mean transferability (A–C) and effect of divergence on transferability (D–F), after first controlling for the effects of native expression level and COG functional category. Each point shows the deviation (i.e., residual) of each gene’s value from the expected value given…
Growth rate is a dominant factor predicting the rhizosphere effect
Rhizosphere bacteria have shorter predicted doubling times than soil bacteria To investigate whether growth rate potential predictions correlate with rhizosphere enrichment, we re-analyzed previously published metacommunities. These included rhizospheres and associated bulk soil microbiomes from 18 different plant genotypes and conditions such as: Arabidopsis thaliana ecotypes and sister species [9],…
The NCI-MATCH trial: lessons for precision oncology
Jabbour, E. & Kantarjian, H. Chronic myelogenous leukemia: 2020 update on diagnosis, therapy and monitoring. Am. J. Hematol. 95, 691–709 (2020). Article CAS PubMed Google Scholar Waarts, M. R., Stonestrom, A. J., Park, Y. C. & Levine, R. L. Targeting mutations in cancer. J. Clin. Invest. 132, e154943 (2022). Article …
Investigation of differences in susceptibility of Campylobacter jejuni strains to UV light-emitting diode (UV-LED) technology
Chlebicz, A. & Slizewska, K. Campylobacteriosis, salmonellosis, yersiniosis, and listeriosis as zoonotic foodborne diseases: A review. Int. J. Environ. Res. Public Health 15, 863 (2018). Article PubMed PubMed Central Google Scholar Soro, A. B., Whyte, P., Bolton, D. J. & Tiwari, B. K. Strategies and novel technologies to control Campylobacter…
Host-adaptive traits in the plant-colonizing Pseudomonas donghuensis P482 revealed by transcriptomic responses to exudates of tomato and maize
P. donghuensis P482 achieved high populations on the roots of soil-grown tomato and maize, confirming it to be a suitable model for studying bacterial adaptations to different hosts P482 Rif was present on the roots of 18-day-old tomato and maize plants grown in soil from inoculated seeds. Based on arithmetic…
Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics
Construction of proteomic content networks from an ultra-deep metaproteomic approach We define the proteomic content network (PCN) of a microbiome sample as a bipartite graph connecting each microbial taxon to all expressed functions from the taxon’s proteome. In order to gain the deepest possible understanding of sample-specific PCN of the…
Infinite value present in GRM, between sample ‘XXXX’ and itself
when I try to run –pca command Iget the Error massge:” Infinite value present in GRM, between sample ‘XXXX’ and itself”what the problem can be?command:../scripts/plink2 –vcf filterxy.vcf.gz –pca allele-wts –exclude pca-clean.prune.out –freq counts –remove pca-clean.king.cutoff.out.id –out pca-clean log: PLINK v2.00a5LM 64-bit Intel (16 May 2023) www.cog-genomics.org/plink/2.0/(C) 2005-2023 Shaun Purcell,…
Group B Streptococcus Cas9 variants provide insight into programmable gene repression and CRISPR-Cas transcriptional effects
Amino acid sequence comparisons between GAS and GBS Cas9 identify orthologous active sites Relationships between the amino acid sequence of GBS Cas9 endonuclease and its molecular functions can be deduced from detailed studies of its GAS ortholog, SpyCas9 (Supplementary Fig. 1). As a first step in locating DNA complementary to a…
Vancomycin intermediate-resistant Staphylococcus haemolyticu | IDR
Wanyang Dong,1,* Qi Peng,1,* Xiaohua Tang,1,2,* Tian Zhong,1 Shunan Lin,1 Ziling Zhi,1 Jingyi Ye,1 Bixia Yang,1 Ning Sun,1,3 Wenchang Yuan1 1Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China; 2Third Affiliated Hospital…
City of Hope Researcher Leads Successful Phase 3 Trial for Hodgkin Lymphoma Treatment
LOS ANGELES and PORTLAND, Ore. — A Phase 3 trial has demonstrated that patients with advanced stage (3 or 4) classic Hodgkin lymphoma who underwent initial treatment with nivolumab, a PD-1 checkpoint inhibitor, and AVD chemotherapy (N-AVD) had a significantly lower risk of their cancer getting worse than patients treated…
Phase 3 SWOG Cancer Research Network trial, led by a City of Hope researcher, demonstrates one-year progression-free survival in 94% of patients with Stage 3 or 4 classic Hodgkin lymphoma who received a checkpoint inhibitor combined with chemotherapy
Nivolumab added to AVD chemotherapy expected to become new standard for initial treatment for advanced stage disease in adolescents and adults, based on trial data to be presented at 2023 American Society of Clinical Oncology (ASCO) Annual Meeting Plenary Session LOS ANGELES and PORTLAND, Ore., June 4, 2023 /PRNewswire/ —…
glm sample size vs OBS_CT
I am running glm with plink2. See code below: PLINK v2.00a3.6 AVX2 (14 Aug 2022) www.cog-genomics.org/plink/2.0/(C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3Logging to /PROJECTES/HELIX_OMICS/analyses/GWAS_chemical_exposure_ZB/results/phthalates_mb/mecpp/mecpp.log.Options in effect: –bfile /PROJECTES/HELIX_OMICS/data_final/gwas/child/8y/GSA_QC3.HRCimp_20210615/HELIX.impQC.rs.05.EUR –covar /PROJECTES/HELIX_OMICS/analyses/GWAS_chemical_exposure_ZB/db/HELIX_phtalates_cov_plink.txt –covar-name PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8,…
Merging multiple PLINK files
Merging multiple PLINK files 0 Hello, I’ve been trying to merge multiple PLINK files (bed bim fam). I have 6 datasets that are genotyped on different genotyping arrays. So technically when I try to merge them using the command plink –bfile dataset1 –merge-list all_lists.txt –make-bed –out merged_data I get multiple…