Tag: COG

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,…

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…

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…

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…

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/ —…

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 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…

I am encountering “Error: Frequency/count too large on line XXX of –read-freq file” when applying a score using plink2.  As far as I can tell, this seems to be happening where the site is multiallelic in the cohort that I’m applying the score in. (The derivation cohort data where the…

PLINK not converting entire vcf to bed file 0 here is my code : [ethan.kreuzer@hydra1 2_Population_stratification]$ plink –vcf ALL.2of4intersection.20100804.genotypes.vcf.gz –make-bed –out ALL.2of4intersection.20100804.genotypes [mii] Please select a module to run plink: MODULE PARENT(S) 1 plink/1.9b_6.21-x86_64 StdEnv/2020 2 plink/1.07 nixpkgs/16.09 intel/2018.3 3 plink/1.9b_5.2-x86_64 nixpkgs/16.09 4 plink/1.9b_4.1-x86_64 nixpkgs/16.09 Make a selection (1-4, q…

Heo J, Cho H, Kim MA, Hamada M, Tamura T, Saitou S, Kim SJ, Kwon SW. Protaetiibacter intestinalis gen. nov., of the family Microbacteriaceae, isolated from gut of Protaetia brevitarsis seulensis, reclassification of Lysinimonas kribbensis Jang et al. 2013 as Pseudolysinimonas kribbensis gen. nov., comb. nov. and emended description of…

Summary of genes and pathways in SMDB Using keywords (e.g., sulfur, sulfate) to retrieve 284,541 literature reports from 1976 to 2021 in Web of Science and then obtained records of sulfur genes through a web crawler with Python. After manual verification, 875 related literature reports (representative literature was recruited) and…

Malaria kills more than half a million people every year, mostly children under the age of five in Africa. Saving the lives of those children was the lifelong mission of Dominic Kwiatkowski, who has died suddenly aged 69. Allied to that ambition was his vision that genetic sequencing – a…

Good afternoon! It’s great to see you getting into bioinformatics. I can definitely help you get started with your linkage disequilibrium (LD) analysis using Plink. Here’s a general workflow to perform LD analysis using Plink with your Saccharomyces cerevisiae samples: First, you need to install Plink if you haven’t already….

La Rosa SL, Ostrowski MP, Vera-Ponce de León A, McKee LS, Larsbrink J, Eijsink VG, Lowe EC, Martens EC, Pope PB (2022) Glycan processing in gut microbiomes. Curr Opin Microbiol 67:102143. doi.org/10.1016/j.mib.2022.102143 CrossRef  CAS  PubMed  Google Scholar  Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette…

Bacterial strains and cultivation Twenty-eight L. paracasei isolates (including L. paracasei Zhang) and a pglX gene-inactivated strain of L. paracasei Zhang were obtained from the Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, at the Inner Mongolia Agricultural University of China. For strain activation, the bacteria were cultivated…

Hello, Can someone please help me with this issue I’m having? Thank you in advance! I have a GFF file, and I have the gene_name attribute in my GFF file, but it’s only present for each gene entry (i.e., it’s absent from the transcript, cds, and exon rows). I want…

Over 1,244 Alzheimer’s patients now enrolled in Phase 3 studies of simufilam. Completion of patient enrollment for Phase 3 program still expected Q4 2023. $187.5 Million Cash and Cash Equivalents at March 31, 2023. AUSTIN, Texas, May 01, 2023 (GLOBE NEWSWIRE) — Cassava Sciences, Inc. (Nasdaq: SAVA), a clinical-stage biotechnology…

Over 1,244 Alzheimer’s patients now enrolled in Phase 3 studies of simufilam. Completion of patient enrollment for Phase 3 program still expected Q4 2023. $187.5 Million Cash and Cash Equivalents at March 31, 2023. AUSTIN, Texas, May 01, 2023 (GLOBE NEWSWIRE) — Cassava Sciences, Inc. (Nasdaq: SAVA), a clinical-stage biotechnology…

Kristina A. Cole, MD, PhD Two recent papers from researchers in the Children’s Hospital of Philadelphia (CHOP) Cancer Center have advanced the understanding of treatment-resistant pediatric tumors, both in assessing a novel treatment and in characterizing the role of alternative lengthening of telomeres (ALT) in these refractory tumors. The first…

Case Reports . 2023 Apr 12;11(4):e7156. doi: 10.1002/ccr3.7156. eCollection 2023 Apr. Affiliations Expand Affiliations 1 Department of Pathology University of California San Francisco USA. 2 Helen Diller Family Comprehensive Cancer Center University of California San Francisco USA. Item in Clipboard Case Reports Alexander Craig et al. Clin Case Rep. 2023. Show…

Blume-Werry G, Krab EJ, Olofsson J, Sundqvist MK, Väisänen M, Klaminder J. Invasive earthworms unlock arctic plant nitrogen limitation. Nat Commun. 2020;11:1766. Article  CAS  PubMed  PubMed Central  Google Scholar  Xing Y, Meng X, Wang L, Zhang J, Wu Z, Gong X, et al. Effects of benzotriazole on copper accumulation and…

Soil water content (SWC) There was a significant difference (p = 0.000367) between the mean SWC across the four treatments. The water content was highest in plots exposed to 100% of the natural precipitation and gradually decreased in plots receiving 75%, 50% and 25% of the natural precipitation (Fig. 1A). The SWC was…

Hi,   I have been using the newest version of PLINK2 (www.cog-genomics.org/plink/2.0/) to perform a sex-SNP interaction analysis with a binary outcome.     I ran the following command:   plink2 –bgen [FILE].bgen –sample [FILE].sample –pheno-name [pheno] –covar [FILE].phen –covar-name sex PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9…

There are several promising new vaccine candidates being developed for complex diseases that historically have been extremely difficult to find treatments and cures for. The development of these new vaccines could eventually lead to breakthrough treatments for diseases such as Alzheimer’s disease, HIV, Parkinson’s disease, Lyme disease, and breast cancer. …

Moeller, A. H. et al. Cospeciation of gut microbiota with hominids. Science 353, 380–382 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  Milani, C. et al. The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol. Mol. Biol. Rev. 81, e00036-17…

Hi all, I am trying to generate a count.matrix for sorted bam files, using featureCounts on linux. I have a non-modal organism (bacteria), so I generated the annotation.file using both PROKKA and RAST. I used all the following files in featurecounts; PROKKA.gff, RAST.gff RAST.gtf gffread converted-PROKKA.gtf file But still facing…

Philadelphia, April 3, 2023—In a significant step for the treatment of neuroblastoma, an international group of researchers led by Children’s Hospital of Philadelphia (CHOP), Winship Cancer Institute of Emory University and the New Approaches to Neuroblastoma Therapy (NANT) Consortium has shown that the targeted therapy lorlatinib is safe and effective in treating…

Passing strings for password, email authentication and download link 0 Hi I am downloading the data from a website which requires authentication of email_id and password before the download. They then provide the download link which is used to download dataset. This download link is different everytime ### Download Cosmic…

How to analize multiple letters codes in COG IDs? 1 Hi Biostars, I’m trying to analize undescribed genes by their functional categories (eggnog) and it would be very helpful to receive suggestions regarding how to deal with these “chimeric” codes such as ‘IQ’, ‘ET’, and ‘EGIPQ’. I’ve read that researchers…

Hello Biostars, I used to use python but I’m not good at it thus I need your help. I’m trying parsing a tab file resulting from the functional annotation using EggNOG-mapper. here. I want to explore all the essential information and make some plots from this data. what I did…

Inagaki, F., Takai, K., Kobayashi, H., Nealson, K. H. & Horikoshi, K. Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing e-proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough. Int. J. Syst. Evol. Microbiol. 53, 1801–1805 (2003). Article  CAS  PubMed  Google Scholar  Timmer-Ten Hoor, A. A new type of…

GBD 2017 Disease and Injury Incidence and Prevalence Collaborators. Global, regional, and national incidence, prevalence, and years lived with disability for 354 diseases and injuries for 195 countries and territories, 1990-2017: a systematic analysis for the Global Burden of Disease Study 2017. Lancet. 2018;392:1789–858. Article  Google Scholar  Smoller JW, Finn…

Abstract The human gut microbiome composition has been linked to Parkinson’s disease (PD). However, knowledge of the gut microbiota on the genome level is still limited. Here we performed deep metagenomic sequencing and binning to build metagenome-assembled genomes (MAG) from 136 human fecal microbiomes (68 PD samples and 68 control…

CARSON CITY, Nev., March 02, 2023 (GLOBE NEWSWIRE) — BioVie Inc. (NASDAQ: BIVI) (“BioVie” or the “Company”), a clinical-stage company developing innovative drug therapies for the treatment of neurological and neurodegenerative disorders and advanced liver disease, today announced that its NM101 trial evaluating NE3107 in the treatment of patients with Alzheimer’s Disease, has achieved…

PRESS RELEASE PUBLICATION OF THE MASITINIB PIVOTAL PHASE 3 CLINICAL TRIAL IN ALZHEIMER’S DISEASE IN THE JOURNAL ALZHEIMER’S RESEARCH & THERAPY Paris, 28 February, 2023, 8am CET AB Science SA (Euronext – FR0010557264 – AB) today announced publication of results from its positive pivotal phase 3 trial (AB09004) of masitinib…

Moore CM, Mills MM, Arrigo KR, Berman-Frank I, Bopp L, Boyd PW, et al. Processes and patterns of oceanic nutrient limitation. Nat Geosci. 2013;6:701–10. Article  CAS  Google Scholar  Sohm JA, Webb EA, Capone DG. Emerging patterns of marine nitrogen fixation. Nat Rev Microbiol. 2011;9:499–508. Article  CAS  PubMed  Google Scholar  Zehr…

Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng J-F, et al. Insights into the phylogeny and coding potential of microbial dark matter nature. Nat Publ Group. 2013;499:431–7. CAS  Google Scholar  Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, et al. Unusual biology across…

Zhang J, Liu Y, Zhang N, Hu B, Jin T, Xu H, et al. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nat Biotechnol. 2019;37:676–84. Article  CAS  PubMed  Google Scholar  Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH. Going back to the roots:…

Alberdi A, Aizpurua O, Bohmann K, Zepeda-Mendoza ML, Gilbert MTP. Do vertebrate gut metagenomes confer rapid ecological adaptation? Trends Ecol Evol 2016;31:689–99. Article  PubMed  Google Scholar  Groussin M, Mazel F, Alm EJ. Co-evolution and co-speciation of host-gut bacteria systems. Cell Host Microbe. 2020;28:12–22. Article  CAS  PubMed  Google Scholar  Alberdi A,…

The loss of RsmQ causes widescale proteomic changes. (a) Comparative scatter plot comparing log2-fold mRNA abundance changes from RNAseq (n = 5) to protein abundance changes seen by TMT quantitative proteomics (n = 3). (b) COG categories of proteins that showed a greater than log2-fold change when rsmQ is lost…

Hi all, I am trying to count the number of reads that map to each gene using FeatureCounts. (RNA-Seq PE, linux) my input; GFF. file generated using Prokka GTF.file generated by NCBI annotation Sorted.bam files generated by bowtie2 and samtools. When I used gtf.file generated by NCBI, featurecounts run without…

Hi everyone, I am currently preprocessing UK Biobank genetic data in order to run a GWAS. I am working with the imputed data, which I transformed to .pgen files and then merged into a single file containing all chromosomes. I have run into a problem with excluding variants with poor…

Viral metagenomics is the study of viruses in environmental and biological samples by utilizing next generation sequencing that generates very large data sets. Viral metagenomics analyzes viral sequences to deduce the impact of viruses on the environment of human health. Unlike amplicon sequencing, metagenomics obtains and investigates genetic material directly…

Functional annotation results with Eggnog mapper, For a same query several COGs, several GO:…. 0 Hello, pleaaaase I need help !!! I performed a fonctionnal annotation for 2 set of transcriptomes with eggnogmapper, the problem is that I don’t really know how to exploit this results .. For example for…

ReportLinker In order to serve several fields of scientific study, including biomedicine, bioinformatics—a mix of biology and information technology—links biological data with methods for information storage, dissemination, and analysis. New York, Jan. 27, 2023 (GLOBE NEWSWIRE) — Reportlinker.com announces the release of the report “Global Bioinformatics Market Size, Share &…

Data collection Metagenomic project information was collected from the MGnify metagenomic database31. Currently (September 2021), microbiome data (sequence, taxonomic, and functional information, etc.) of 325,323 environmental samples can be found in this database. Often, microbes from similar ecological communities have been studied by different groups at different times and locations….

Changes of straw degradation characteristics at different culture stages Corn straw degradation ratio Corn straw weight loss in M44 at F1 reached 35.90% at 15 ℃ for 21 days, which was greater than that at F5, F8, and F11 by 2.33%, 3.01%, and 3.35%, respectively. There were no significant differences between…

Study cohort description We used data on a total of 172,270 individuals of Japanese and East Asian ancestry. Of these, data on 165,098 individuals were obtained from BBJ, which has enrolled ≥200,000 participants to date. BBJ is a multi-institutional hospital-based genome cohort that collected participants affected with at least one…

Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017). CAS  PubMed  Article  Google Scholar  Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J. & Embley, T. M. Phylogenomics provides robust support for a two-domains tree of life. Nat. Ecol….

Allfrey, V. G., Faulkner, R. & Mirsky, A. E. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc. Natl Acad. Sci. USA 51, 786–794 (1964). CAS  PubMed  PubMed Central  Google Scholar  Ho, J. W. K. et al. Comparative analysis of metazoan chromatin organization….

Control: reopen -1 Control: tags -1 confirmed Control: tags -1 upstream Control: forwarded -1 Christopher Chang <chrch…@alumni.caltech.edu> Hi Christopher (and Dylan), I verified the latest version (29 Jan 2022) of plink2 with the same result for the CI test we are doing in Debian (which was written by Dylan): $…

I’m using the software plink2 (www.cog-genomics.org/plink/2.0/) and I’m trying to iterate over 3 variables. This software admits an input file with .ped extention file and an exclude file with .txt extention which contains a list of names to be excluded from the input file. The idea is to iterate over…

33.3.1.3 Oil Field Microbiology: Asia Oilfields in Russia and China have been extensively studied to determine microbial ecology as well as understand the microbial community for bioprospecting aspects. Molecular approaches as well as radioisotopic activity measurements from formation water of a high temperature oil reservoir in Russia (Samotlor) indicated enrichment…

Hi all, I have recently tried to estimate runs of homozygosity (ROH) from my vcf file by using plink 1.9. I ran following code to generate binary files that plink required: plink –vcf myfile.vcf –make-bed –out out_name –no-sex –no-parents –no-fid –no-pheno –allow-extra-chr This vcf file only contains one individual and…

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…

1. Szathmáry E, Smith JM. The major evolutionary transitions. Nature 1995;374:227–32. PubMed  Google Scholar  2. West SA, Fisher RM, Gardner A, Kiers ET. Major evolutionary transitions in individuality. Proc Natl Acad Sci USA. 2015;112:10112–9. CAS  PubMed  PubMed Central  Google Scholar  3. Moran NA. The coevolution of bacterial endosymbionts and phloem-feeding…

Cutoffs for Proxy Identification: D’ and R^2 0 I’m using a proxy-finding script with plink that reports potential proxies with their D’ and R^2: proxy D’ R^2 9:12345698:rs12345 1.0 0.000758121 9:12345999:rs87654 1.0 0.039958 9:12346999:rs54321 1.0 0.0399958 cf. www.cog-genomics.org/plink/2.0/ld However, what cutoffs should be used? From what I’ve read, D’ is…

Northumbria University is a member of the COVID-19 Genomics UK Consortium (COG-UK).  COG-UK is a pioneer in the use of large-scale, rapid whole-genome sequencing of SARS-CoV-2, the virus causing the COVID-19 pandemic, to understand viral transmission and evolution, and to inform public health responses and vaccine development. We seeking to…

Problem merging data in plink 1 welcome everybody… In short, this is the error message that appears: Error: 4 variants with 3+ alleles present. If you believe this is due to strand inconsistency, try –flip with merge-merge.missnp. (Warning: if this seems to work, strand errors involving SNPs with A/T or…

  linkage disequilibrium and haplotype analysis of GWAS . 0   Hi all, I have GWAS data. I have my data in 22 chromosome files in plink format. I have imputed genotype with Sanger imputation server. I use plink for my analysis but because plink 1.9 no more supports –hap…

Download COG Database 0 How to extract COG database for GAMMAPROTEOBACTERIA? database COG • 27 views Login before adding your answer. Source link

formatting error: Calculate LD matrix from bgen file 1 Hello, I am new to plink and am learning as I go. I am trying to calculate an LD matrix for a list of variants while using a bgen file as my reference population. See the command below: ./plink2/plink2 –r2 bin…

I have an S4 object named ‘res’ which I got while using an R package called RDAVIDWebService. I can’t seem to find a way to convert this object into a dataframe in R. I tried using the function ‘as.data.frame(res)’ but it throws this error: > as.data.frame(res) Error in as.data.frame.default(res) :…