Tag: EggNOG

What statistical test should I use to analyse my two set of transcriptomique data? 0 I have an assembled transcriptome. I performed analyses on this transcriptome to extract candidate sequences involved in the production of a substance. Then, I annotated both sets of data using the Eggnog Mapper tool. This…

Genome sequencing and assembly We sequenced and assembled genomes for the sandalwood species S. album and S. yasi (Fig. 1). In total, ~23 Gb and ~25 Gb of clean short reads of S. album and S. yasi were obtained for the genomic survey, respectively (Supplementary Tables 1 and 2). According to k-mer analysis, the…

Hunt, T. et al. A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science 318, 1913–1916 (2007). Article  ADS  CAS  PubMed  Google Scholar  Crowson, R. A. The phylogeny of coleoptera. Annu. Rev. Entomol. 5, 111–134 (1960). Article  Google Scholar  Darwin, C. The Descent of Man, and Selection…

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…

Welch, J. L. M., Dewhirst, F. E. & Borisy, G. G. Biogeography of the oral microbiome: The site-specialist hypothesis. Annu. Rev. Microbiol. 73, 335–358. doi.org/10.1146/annurev-micro-090817-062503 (2019). Article  CAS  Google Scholar  Cornejo Ulloa, P., van der Veen, M. H. & Krom, B. P. Review: Modulation of the oral microbiome by the…

Manrique, P., Dills, M. & Young, M. J. The human gut phage community and its implications for health and disease. Viruses 9, 141 (2017). Article  PubMed  PubMed Central  Google Scholar  Li, Z. et al. Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. ISME J….

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…

Ashton PM, Nair S, Dallman T et al (2015) MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat Biotechnol 33:296–302 CrossRef  CAS  PubMed  Google Scholar  Fenn JB, Mann M, Meng CK et al (1990) ChemInform abstract: electrospray ionization for mass spectrometry of large biomolecules….

Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, et al. Global organization and proposed megataxonomy of the virus world. Microbiol Mol Biol Rev. 2020;84:e00061–19. Article  CAS  PubMed  PubMed Central  Google Scholar  Wilhelm S, Bird J, Bonifer K, Calfee B, Chen T, Coy S, et al. A…

Ma, Y. et al. Gut microbiota adaptation to high altitude in indigenous animals. Biochem. Biophys. Res. Commun. 516, 120–126 (2019). Article  CAS  PubMed  Google Scholar  Guo, N. et al. Seasonal dynamics of diet-gut microbiota interaction in adaptation of yaks to life at high altitude. NPJ Biofilms Microbiomes 7, 38 (2021)….

Vincent, F., Sheyn, U., Porat, Z., Schatz, D. & Vardi, A. Visualizing active viral infection reveals diverse cell fates in synchronized algal bloom demise. Proc. Natl Acad. Sci. USA 118, e2021586118 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  Suttle, C. A. Marine viruses — major players in the global…

Media The minimal marine media, MBL media, was used for serial dilution growth of Tritonibacter mobilis A3R06. It contained 10 mM NH4Cl, 10 mM Na2HPO4, 1 mM Na2SO4, 50 mM HEPES buffer (pH 8.2), NaCl (20 g/liter), MgCl2*6H2O (3 g/l), CaCl2*2H2O (0.15 g/l), and KCl (0.5 g/l). Glucose was added as the only carbon source at a…

Philippi M, Kitzinger K, Berg JS, Tschitschko B, Kidane AT, Littmann S, et al. Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue. Nat Commun. 2021;12:4774. Article  CAS  PubMed  PubMed Central  Google Scholar  Xiong Y, Guilbaud R, Peacock CL, Cox RP, Canfield DE, Krom MD,…

Handa IT, Aerts R, Berendse F, Berg MP, Bruder A, Butenschoen O, et al. Consequences of biodiversity loss for litter decomposition across biomes. Nature. 2014;509:218–21. Article  CAS  PubMed  Google Scholar  Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, et al. Minimum information about an uncultivated virus…

Comprehensive protein function annotation is essential for understanding microbiome-related disease mechanisms in the host organisms. However, a large portion of human gut microbial proteins lack functional annotation. Here, we have developed a new metagenome analysis workflow integrating de novo genome reconstruction, taxonomic profiling, and deep learning-based functional annotations from DeepFRI….

1. Introduction Fusarium fungi are world-wide producers of a range of mycotoxins. Deoxynivalenol (DON) belonging to the group B trichothecenes, is one of the most prevalent food-associated mycotoxins mainly produced by Fusarium graminearum and Fusarium culmorum, and frequently contaminates cereals and cereal products [1,2]. Almost half of a total of…

Fungi, ain’t a kingdom most of us will know much about. The only thing I can guess at is that in bacteria there has resurgence in methods for de novo assembly specifically aimed at reducing the total number of contigs in an assembly. The ‘new wave’ is summarised in this…

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…

Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, et al. Evolution of mammals and their gut microbes. Science. 2008;320:1647–51. Article  CAS  PubMed  PubMed Central  Google Scholar  Ochman H, Worobey M, Kuo CH, Ndjango JB, Peeters M, Hahn BH, et al. Evolutionary relationships of wild hominids recapitulated…

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…

Gene Enrichment analysis with EggNog output 0 Hi everyone! I want to perform a gene set enrichment analysis of differently expressed host genes during virus infection. I performed Gene Ontology (GO) annotation with eggnog for the whole host genome and got one .tsv file, an excel file, and two .orthologs…

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:…

Forum:What to do if hundreds or genes have no functional domain! 0 Hi! I did functional annotation (using KEGG, eggNOG, TRAPID, NR,Uniprot, and Mercator) of 5 cultivars (plants) to do my analysis. Long story short I identified genes that are private to each cultivar. Almost 70% genes in every cultivar…

Gene names/ids on annotated protein files 0 Hello all, I have annotated around 276 protein files using EggNog. The protein files have the following headers (example from one of the species): head Spodoptera_frugiperda.fa file_1_file_1_g22553.t1 gene=file_1_file_1_g22553 MNRLGMIVDLSHVGENTTRAAIKLSRAPVVFTHSSVYSLCNHKRNVPDDIIHSLKENGGIIMVNFFPDFVKCAPNATISDVAEHFHYIKRMVGADYVGIGGDFDGVNRVPRGLEDVSRYPELFAELLRSGQWTVQELKNLAGLNMLRVMRQVEKVRDEMRTNGVEPEEHPDSPNDNGNCTSNAFYTEYV The annotation file from EggNog has the following: head Spodoptera_frugiperda.softmasked.prot.fa.emapper.annotations file_1_file_1_g22553.t1 13037.EHJ66618 2.39e-121 357.0…

I’m trying to work out is how reliable/accurate my eggNOG metagenomic outputs are. Critical for this is how its identifying orthologues. Background eggNOG is commonly used in metagenomics gene identification. Take a sample, randomly sequence all the DNA therein, then “annotate” via eggNOG. It identifies the putative gene function against…

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…

Materials Medakamo hakoo 311 was obtained from the personal aquarium of Prof. Kuroiwa (Kagurazaka, Tokyo, Japan)4. The M. hakoo strain was cultured in 0.05% HYPONeX (HYPONeX Japan Corp., Ltd., Osaka, Japan) liquid medium and on 0.05% HYPONeX gellan gum-based solid medium in plates. Cyanidioschyzon merolae 10D (Toda et al. 1995)…

Merlino, C. P. Bartolomeo Bizio’s letter to the most eminent priest, Angelo Bellani, concerning the phenomenon of the red-colored polenta [translated from the Italian]. J. Bacteriol. 9, 527–543 (1924). Grimont, P. A. D. & Dulong de Rosnay, H. L. C. Numerical study of 60 strains of Serratia. J. Gen. Microbiol….

Salje, J. Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle. Nat. Rev. Microbiol. 19, 375–390 (2021). CAS  PubMed  Article  Google Scholar  Wang, S. & Luo, H. Dating Alphaproteobacteria evolution with eukaryotic fossils. Nat. Commun. 12, 3324 (2021). CAS  PubMed  PubMed Central  Article  Google Scholar  Strassert, J. F. H.,…

Introduction The study of the microbial environments has benefited from the sequencing revolution, where technology improvement decreased the DNA sequencing cost and increased the number of sequenced nucleic bases. For approximately 20 years (depending on how we define the term metagenomics), it has allowed the decryption of the microbial composition…

You can do this directly on UniProt: www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select “UniProtKB AC/ID” in the “From” field and “UniParc” in the “To” field I’ve also written a script, pasted below, that can do this with some useful options: $ uniprot_map.pl -h uniprot_map.pl…

INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…

What exactly is the error you are seeing? You shouldn’t set sys.sterr and sys.stdout to string values (the clustalw_cline() function returns the clustal stderr and stdout as strings), as you won’t be able to write anything to stdout from python. I tried to clean up and correct your code below….

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1. Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015). PubMed  Google Scholar  2. Zou, Y. et al. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. Nat. Biotechnol. 37, 179–185 (2019). CAS  PubMed  PubMed Central  Google Scholar  3. Mohammad,…

What is the best tool to recover nitrogen cycling genes from an annotated assembly? 0 I have annotated metagenomic assemblies and am wanting to recover genes involved in the nitrogen cycle. I have identified three tools to help me do this but I unsure how to go about selecting them…

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