Tag: antiSMASH

Contigs number vs NNN gap % in WGS

Contigs number vs NNN gap % in WGS 0 Hi all, I have two fasta files of bacterial whole genome sequence assembly (same genome) generated by spades generated by spades > extra scaffolding step using multi-csar, by comparing it to 5 close genomes. quast statistics as below : Genome 1…

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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…

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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…

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Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses

Honegger, R. The lichen symbiosis: What is so spectacular about it?. Lichenologist 30, 193–212 (1998). Article  Google Scholar  Grube, M. & Berg, G. Microbial consortia of bacteria and fungi with focus on the lichen symbiosis. Fung. Biol. Rev. 23, 72–85 (2009). Article  Google Scholar  Spribille, T. et al. Basidiomycete yeasts…

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Genome mining reveals novel biosynthetic gene clusters in entomopathogenic bacteria

Katz, L. & Baltz, R. H. Natural product discovery: Past, present, and future. J. Ind. Microbiol. Biotechnol. 43, 155–176 (2016). Article  CAS  PubMed  Google Scholar  Newman, D. J. & Cragg, G. M. Natural products as sources of new drugs from 1981 to 2014. J. Nat. Prod. 79, 629–661 (2016). Article …

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Draft genome sequencing of halotolerant bacterium Salinicola sp. DM10 unravels plant growth-promoting potentials

Afridi MS, Amna S et al (2019) Induction of tolerance to salinity in wheat genotypes by plant growth promoting endophytes: Involvement of ACC deaminase and antioxidant enzymes. Plnat Physiol Biochem 139:569–577. doi.org/10.1016/j.plaphy.2019.03.041 Article  CAS  Google Scholar  Ali S, Charles TC, Glick BR (2014) Amelioration of high salinity stress damage by…

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Identification of peptides from honeybee gut symbionts as potential antimicrobial agents against Melissococcus plutonius

Khalifa, S. A. M. et al. Overview of bee pollination and Its economic value for crop production. Insects 12 (2021). Vanengelsdorp, D. et al. Colony collapse disorder: a descriptive study. PLoS ONE 4, e6481 (2009). Article  ADS  PubMed  PubMed Central  Google Scholar  Muli, E. et al. Evaluation of the distribution…

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facing Issue while runing the CORASON command line

facing Issue while runing the CORASON command line 0 I want to use the CORASON command line to derive the phylogenetic tree for one of the selected secondary metabolite from bacterial genomes. I previously ran antiSMASH to get the BGCs from bacterial genomes and used BiG-SCAPE to get the gene…

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Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis

Neilson, J. W. et al. Significant impacts of increasing aridity on the arid soil microbiome. mSystems 2, e00195–e00116 (2017). Article  CAS  PubMed  PubMed Central  Google Scholar  Fierer, N. et al. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc. Natl Acad. Sci. USA 109, 21390–21395 (2012). Article …

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Isolation of Spirosoma foliorum sp. nov. from the fallen leaf of Acer palmatum by a novel cultivation technique

Locey, K. J. & Lennon, J. T. Scaling laws predict global microbial diversity. PNAS 113, 5970–5975. doi.org/10.1073/pnas.1521291113 (2016). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Hahn, M. W., Koll, U. & Schmidt, J. The Structure and Function of Aquatic Microbial Communities (Springer International Publishing, 2019). Rosenberg, E., DeLong, E….

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Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte: Alternaria burnsii NCIM 1409

Atanasov, A. G. et al. Discovery and resupply of pharmacologically active plant-derived natural products: A review. Biotechnol. Adv. 33, 1582–1614 (2015). Article  CAS  PubMed  PubMed Central  Google Scholar  Swamy, M. K. et al. Biotechnology of camptothecin production in Nothapodytes nimmoniana, Ophiorrhiza sp. and Camptotheca acuminata. Appl. Microbiol. Biotechnol. 105, 9089–9102…

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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…

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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…

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Saccharopolyspora oryzae sp. nov., isolated from rhizosphere soil of the wild rice species Oryza rufipogon

Lacey J, Goodfellow M. A novel actinomycete from sugar-cane bagasse: Saccharopolyspora hirsuta gen. et sp. nov. Microbiol. 1975;88:75–85. CAS  Google Scholar  Warwick S, Bowen T, McVeigh H, Embley TM. A phylogenetic analysis of the family Pseudonocardiaceae and the genera Actinokineospora and Saccharothrix with 16S rRNA sequences and a proposal to…

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Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle

Bond PL, Hugenholtz P, Keller J, Blackall LL. Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl Environ Microbiol. 1995;61:1910–6. Article  CAS  PubMed  PubMed Central  Google Scholar  Wang Z, Guo F, Liu L, Zhang T. Evidence of carbon fixation pathway in a bacterium from candidate…

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Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host

Fragoso Ados Santos, H. Impact of oil spills on coral reefs can be reduced by bioremediation using probiotic microbiota. Sci. Rep. doi.org/10.1038/srep18268 (2015). Article  PubMed  PubMed Central  Google Scholar  Silva, D. P. et al. Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and…

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Input format for BiG-SLiCE

Input format for BiG-SLiCE 0 Hi, I have used the antiSMASH program to derive the biosynthetic gene cluster (BGC) from analyzing bacterial genome. At present, I want to use BiG-SLiCE program to cluster the homologous BGCs into Gene Cluster Families (GCFs). I would like to know if anyone can help…

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The genome of antibiotic-producing colonies of the Pelagophyte alga Chrysophaeum taylorii reveals a diverse and non-canonical capacity for secondary metabolism

Keffer, J. L. et al. Geographic variability and anti-Staphylococcal activity of the chrysophaentins and their synthetic fragments. Mar. Drugs 10, 1103–1125 (2012). Article  PubMed  PubMed Central  Google Scholar  Lobban, C. S. & Tsuda, R. T. Revised checklist of benthic marine macroalgae and seagrasses of Guam and Micronesia. Micronesica 35–36, 54–99…

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Genomic characteristics of a multidrug-resistant E. coli

Introduction Escherichia coli, a member of the Enterobacterales family, is a common opportunistic pathogen that can cause various infectious illnesses, including urinary tract infections (UTIs) and other infections acquired in the community.1,2 The presence of carbapenemases in E. coli poses a serious threat to public health. These carbapenemase genes may…

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Comparative genome features and secondary metabolite biosynthetic potential of Kutzneria chonburiensis and other species of the genus Kutzneria

Adamek, M., Spohn, M., Stegmann, E. & Ziemert, N. Mining bacterial genomes for secondary metabolite gene clusters. Methods Mol. Biol. 1520, 23–47 (2017). CAS  PubMed  Google Scholar  Belknap, K. C., Park, C. J., Barth, B. M. & Andam, C. P. Genome mining of biosynthetic and chemotherapeutic gene clusters in Streptomyces…

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Distribution and diversity of ‘Tectomicrobia’, a deep-branching uncultivated bacterial lineage harboring rich producers of bioactive metabolites

Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev. 1995;59:143–69. CAS  PubMed  PubMed Central  Google Scholar  Konstantinidis K, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J. 2017;11:2399–406. PubMed  PubMed Central  Google Scholar  Parks…

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Protaetiibacter mangrovi sp. nov., isolated from mangrove soil

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…

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antiSMASH give poor result about aflatoxin gene cluster visualization.

antiSMASH give poor result about aflatoxin gene cluster visualization. 1 I guess this really depends on what aflatoxin gene cluster you use as input, and probably on what you expect on the visualisation side. In my (arguably biased) opinion, on an aflatoxin cluster like AB196490.1, antiSMASH finds and annotates the…

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JoF | Free Full-Text | Genome Sequencing and Analysis Reveal Potential High-Valued Metabolites Synthesized by Lasiodiplodia iranensis DWH-2

Lasiodiplodia belongs to the fungal family Botryosphaeriaceae, which thrives on a wide range of monocotyledonous, dicotyledonous, and gymnosperm hosts, on woody branches, herbaceous leaves, and grasses, causing die-back and canker diseases in numerous woody hosts [1], such as Mangifera indica [2], Prunus persica [3], Saccharum officinarum [4], and Vitis vinifera…

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Genome-resolved metagenomics revealed metal-resistance, geochemical cycles in a Himalayan hot spring

Agency for Toxic Substances and Disease Registry (ATSDR) (2002) Toxicological profile for copper. Atlanta, GA: Centers for Disease Control Ahemad M (2012) Implications of bacterial resistance against heavy metals in bioremediation: A review. IIOAB J 3:39–46 CAS  Google Scholar  Alcamán-Arias ME, Pedrós-Alió C, Tamames J, Fernández C, Pérez-Pantoja D, Vásquez M,…

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Chemical and genomic characterization of a potential probiotic treatment for stony coral tissue loss disease

Precht, W. F., Gintert, B. E., Robbart, M. L., Fura, R. & van Woesik, R. Unprecedented disease-related coral mortality in Southeastern Florida. Sci. Rep. 6, 31374 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  Knowlton, N. et al. Rebuilding coral reefs: a decadal grand challenge. 1–55 doi.org/10.53642/NRKY9386 (2021). Walton, C….

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Antismash on Fasta files

Hello, you can provide FASTA files to it ########### antiSMASH 6.1.1 ############# usage: antismash [–taxon {bacteria,fungi}] [–output-dir OUTPUT_DIR] [–output-basename OUTPUT_BASENAME] [–reuse-results PATH] [–limit LIMIT] [–minlength MINLENGTH] [–start START] [–end END] [–databases PATH] [–write-config-file PATH] [–without-fimo] [–executable-paths EXECUTABLE=PATH,EXECUTABLE2=PATH2,…] [–allow-long-headers] [-v] [-d] [–logfile PATH] [–list-plugins] [–check-prereqs] [–limit-to-record RECORD_ID] [-V] [–profiling] [–skip-sanitisation] [–skip-zip-file]…

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Nanopore Sequencing Discloses Compositional Quality of Commercial Probiotic Feed Supplements

Morelli, L. & Capurso, L. FAO/WHO guidelines on probiotics: 10 years later. J. Clin. Gastroenterol. 46, S1–S2 (2012). Article  PubMed  Google Scholar  Arsène, M. M. J. et al. The use of probiotics in animal feeding for safe production and as potential alternatives to antibiotics. Vet World 14, 319–328 (2021). Article …

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Hybrid de novo genome assembly and comparative genomics of three different isolates of Gnomoniopsis castaneae

Crous, P. et al. Fungal planet description sheets: 107–127. Pers. Mol. Phylogeny Evol. Fungi 28, 138–182. doi.org/10.3767/003158512X652633 (2012). Article  CAS  Google Scholar  Visentin, I. et al. Gnomoniopsis castanea sp. nov. (Gnomoniaceae, Diaporthales) as the causal agent of nut rot in sweet chestnut. J. Plant Pathol. 94, 411–419. doi.org/10.4454/JPP.FA.2012.045 (2012). Article …

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Seasonal activities of the phyllosphere microbiome of perennial crops

Robertson, G. P. et al. Cellulosic biofuel contributions to a sustainable energy future: Choices and outcomes. Sci. (80-.) 356, 1–9 (2017). Article  Google Scholar  Ma, L. et al. The impact of stand age and fertilization on the soil microbiome of Miscanthus × giganteus. Phytobiomes J. 5, 51–59 (2021). Article  Google…

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A first insight into the Polish Bochnia Salt Mine metagenome

Sequencing statistics NGS was used across the V3-V4 region of the 16S rRNA gene to sequence 24 environmental samples. The mean number of ASVs per sample obtained after DADA2 was 72,050 ± 31,480, ranging from 22,568 to 143,267. From a total of 1,729,209 contigs remaining after quality control and removal of chimeras,…

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Virulence and antibiotic-resistance genes in Enterococcus faecalis associated with streptococcosis disease in fish

Isolation, phenotypic identification, pathogenicity and antibiogram profiling Enterococcus faecalis strains BFF1B1, BFFF11 and BFPS6 were cultured in Streptococcus selective agar media (Himedia, India). The culture characteristics such as colony, morphological, physiological and biochemical characteristics of these strains BFF1B1, BFFF11 and BFPS6 were summarized in the Supplementary Table S1. All of…

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Postdoctoral Research Associate – Bioinformatics – Northeastern University

About the Opportunity We are seeking a creative scientist with a background in computational biology and microbiology to work on a genomics analysis-based antibiotic discovery project. The successful applicant will join a team of talented researchers at the Antimicrobial Discovery Center. Several drug lead candidates came out of our lab…

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CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes

Development of the CusProSe software CustomProteinSearch (CusProSe) is a generic genome mining software, consisting of two distinct but complementary customizable programs: IterHMMBuild and ProSeCDA. IterHMMBuild is an HMM profile building tool based on an iterative learning process. ProSeCDA is a protein search and annotation tool based on user-defined domain architectures….

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biopython – Parsing a gene bank file and outputting specific feature information to a csv using Bio Python

So I am trying to parse through a gene bank file, extract particular feature information and output that information to a csv file. The example gene bank file looks like this: SBxxxxxx.LargeContigs.gbk LOCUS scaffold_31 38809 bp DNA UNK 01-JAN-1980 DEFINITION scaffold_31. ACCESSION scaffold_31 VERSION scaffold_31 KEYWORDS . SOURCE . ORGANISM…

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Postdoctoral Research Associate – Bioinformatics in Boston, MA for Northeastern University

Details Posted: 13-Jul-22 Location: Boston, Massachusetts Type: Full-time Salary: Open Postdoctoral Research Associate – Bioinformatics About the Opportunity We are seeking a creative scientist with a background in computational biology and microbiology to work on a genomics analysis-based antibiotic discovery project. The successful applicant will join a team of talented…

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Postdoctoral Research Associate – Bioinformatics job with Northeastern University

Postdoctoral Research Associate – Bioinformatics About the Opportunity We are seeking a creative scientist with a background in computational biology and microbiology to work on a genomics analysis-based antibiotic discovery project. The successful applicant will join a team of talented researchers at the Antimicrobial Discovery Center. Several drug lead candidates…

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Bacterial endosymbionts protect beneficial soil fungus from nematode attack

A healthy soil nourishes plants and animals, purifies water and air, and promotes sustainable agriculture. Characteristic for highly complex and competitive soil ecosystems are the frequent and direct interactions between all soil-dwelling microorganisms, animals, and plants (1, 2), all of which need to be provided with minerals and carbon sources….

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parsing gbk files (antismash result)

parsing gbk files (antismash result) 0 Hello I used antismash from the CLI and I got 700 gbk files (1 gbk file per each analyzed genome). I used the following script to retrieve the predicted products from the gbk files: from Bio import SeqIO import glob for files in glob.glob(“*.gbk”):…

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antiSMASH output

antiSMASH output 0 Hello. Can someone help me to interpret the antiSMASH output and the count number of BGCs by using command line. It would be great to receive your help. Thank you RESULTS antiSMASH • 65 views Login before adding your answer. Source link

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STAR rna-seq for bacterial genomes

Hi, I’m willing to use STAR for bacterial genomes. I wanted to ask if this is strongly unadvised or if there is a way to manage the main challenges of mapping reads to prokaryotes. (I know there are specific tools for this purpose, i.e. EdgePro, but I’m a beginner in…

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