ncbi datasets command line tools (Biotechnology Information)

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Biotechnology Information ncbi datasets command line tools
Ncbi Datasets Command Line Tools, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/command+line/biotechnology+datasets+information+ncbi/pm42247255-49-71-69
Average 86 stars, based on 1 article reviews

ncbi datasets command line tools - by Bioz Stars, 2026-10

86/100 stars

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Inhibition:

Article Title: Genome mining of amylases and amylase inhibitors from Streptomyces .
Article Snippet: .. BGCs encoding amylase inhibitors were typically found alongside multiple amylases, including variants with amino acid motifs known to provide resistance to inhibition [16] as well as putative resistance variants. mETHoDS Phylogenetic analysis of amylases in Streptomyces A database of 295 Streptomyces genomes [21] (accession numbers found in File S6) was used for the analysis and the protein fasta files for each genome were downloaded with the National Center for Biotechnology Information (NCBI) datasets command- line tools (script: File S10, available in the online Supplementary Material). ..

Sequencing:

Article Title: Challenges and considerations for whole-genome-based antimicrobial resistance plasmid investigations
Article Snippet: SeqSphere+ ( ) , 2024 , Real-time plasmid transmission detection pipeline based on Mash distance. Includes plasmid reconstruction and typing using MOB-suite. Users can visualize output on the same platform. Available as a desktop application. Accessible at: https://www.ridom.de/seqsphere/u/Long-read_Data_Plasmid_Transmission_Analysis_Module.html. .. National Center for Biotechnology Information (NCBI) , N/A , NCBI nucleotide database for general genome sequence queries and download. Users can restrict search to “Genetic compartments: Plasmid” for the desired species or genus. Command line utility ( ncbi-genome-download ) available to download sequences with customizable parameters. Accessible at: https://www.ncbi.nlm.nih.gov/nucleotide/. .. PLSDB ( , ) , 2019 , Open access database containing plasmid sequences retrieved from NCBI Nucleotide. Sequence metadata is available for download. Users can upload their own plasmid FASTA sequence and search for similar matches using the BLAST utility. Metadata filtering is available. The database was last updated on 31 May 2024. Accessible at: https://ccb-microbe.cs.uni-saarland.de/plsdb/.

Article Title: Shifts in bee diet breadths are associated with gene gains and losses and positive selection across olfactory receptors
Article Snippet: .. We queried the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database for available WGS datasets for bee species ( N = 49) alongside data for the clonal raider ant Ooceraea biroi (accessed February-March 2021) using the SRA Toolkit v.2.10.0 command line functions ( ) (see for SRA accession information and citations for previously generated datasets used). ..

Plasmid Preparation:

Whole Complete genome sequencing:

Generated:

other:

Article Title: Antimicrobial resistance databases: opportunities and challenges for public health
Article Snippet: AMRFinderPlus , National Center for Biotechnology Information , Proteins, genes and point mutations, reference gene hierarchy and reference hidden markov models , Antibiotics, stress (disinfecting agents and antiseptics, heat, metal), virulence , 9900 , Manual curation of literature searches, communication with experts, Lahey and Pasteur β-lactamase databases and CARD and ResFinder and PointFinder, automated QC checks , Yes, for mutations in some species , No , Version 4.0.1 (18th December 2024) , 2-4 months , https://github.com/ncbi/amr/wiki/AMRFinderPlus-database , AMRFinderPlus (command-line based, Galaxy servers) , , , .

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