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Biotechnology Information command line tools
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+tools/command+line+tools/pmc12815946-63-30-20
Average 86 stars, based on 1 article reviews
command line tools - by Bioz Stars, 2026-10
86/100 stars

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Related Articles

Sequencing:

Article Title: Wild and globally traded ornamental aquatic plants harbor diverse plant viruses, including notable crop pathogens.
Article Snippet: .. The raw read data were acquired from the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) database using the wget command and data accession links (accessed 2022-12-08). ..

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/.

Plasmid Preparation:

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/.

other:

Article Title: The feeding behaviour of the European pond turtle (Emys orbicularis, L. 1758) is not a threat for other endangered species
Article Snippet: De novo assembly of amplicons per respective sample sequencing data was 211 performed using the genome assembly open software "SPAdes 3.11" (Nurk et al. 2017), 212 deleted and resulting contigs files were then blasted on the server of the National Center 214 for Biotechnology Information (NCBI) using the BLAST+ suite of command line tools 215 (Camacho et al., 2008), against the complete NCBI nucleotide (nr/nt) collection.

Article Title: Do Babesia microti Hosts Share a Blood Group System Gene Ortholog, Which Could Generate an Erythrocyte Antigen That Is Essential for Parasite Invasion?
Article Snippet: More than 600 animals with at least one hBG system gene ortholog were identified using the National Center for Biotechnology Information (NCBI) command-line tools.



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