Tag: antiSMASH
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…
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…
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…
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…
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…
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…
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,…
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….
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]…
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 …
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 …
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…
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,…
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…
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…
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….
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…
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…
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…
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….
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”):…
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
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…
