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draft genome annotation  (DOE Systems Biology Knowledgebase)

 
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    DOE Systems Biology Knowledgebase draft genome annotation
    Draft Genome Annotation, supplied by DOE Systems Biology Knowledgebase, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/draft+genome+annotation/10__1128_slash_aem__01851___20-294-0-12?v=DOE+Systems+Biology+Knowledgebase
    Average 90 stars, based on 1 article reviews
    draft genome annotation - by Bioz Stars, 2026-06
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    Core genome phylogenetic tree depicting Sneathia vaginalis isolates WSU1, WSU2, and WSU4 compared to the six publicly available Sneathia spp. genomes excluding metagenome-assembled genomes. All assemblies were annotated with PGAP version 2024-04-27.build7426. Core genes of these genomes were computed in EDGAR version 3.2 by checking for reciprocal best BLAST hits against all other genomes with Sneathia vaginalis Sn35 as the reference genome . Alignments of each core gene set were generated with MUSCLE and concatenated . A phylogenetic tree was constructed with the neighbor-joining algorithm as implemented in the PHYLIP package . To verify the tree topology, 1,000 bootstrap iterations were calculated. Branch support was above 85.5% for all branches, with all but three showing 100% support. The core consisted of 433 genes per genome in 13 genomes (5,629 genes in total). The core alignment had 175,990 amino acid residues (2,287,870 residues in total). GenBank accession numbers are given in square brackets. Sneathia spp. isolated from vaginal swabs were highlighted in bold. Three genomes from the closely related genus Oceanivirga and a Fusobacterium nucleatum genome were included for comparison. Bar length is equivalent to 0.01 nucleotide substitutions per site.

    Journal: Microbiology Resource Announcements

    Article Title: Draft genomes of three Sneathia vaginalis isolates from a patient with bacterial vaginosis

    doi: 10.1128/mra.00941-24

    Figure Lengend Snippet: Core genome phylogenetic tree depicting Sneathia vaginalis isolates WSU1, WSU2, and WSU4 compared to the six publicly available Sneathia spp. genomes excluding metagenome-assembled genomes. All assemblies were annotated with PGAP version 2024-04-27.build7426. Core genes of these genomes were computed in EDGAR version 3.2 by checking for reciprocal best BLAST hits against all other genomes with Sneathia vaginalis Sn35 as the reference genome . Alignments of each core gene set were generated with MUSCLE and concatenated . A phylogenetic tree was constructed with the neighbor-joining algorithm as implemented in the PHYLIP package . To verify the tree topology, 1,000 bootstrap iterations were calculated. Branch support was above 85.5% for all branches, with all but three showing 100% support. The core consisted of 433 genes per genome in 13 genomes (5,629 genes in total). The core alignment had 175,990 amino acid residues (2,287,870 residues in total). GenBank accession numbers are given in square brackets. Sneathia spp. isolated from vaginal swabs were highlighted in bold. Three genomes from the closely related genus Oceanivirga and a Fusobacterium nucleatum genome were included for comparison. Bar length is equivalent to 0.01 nucleotide substitutions per site.

    Article Snippet: The annotated draft genomes of Sneathia vaginalis isolates WSU1, WSU2, and WSU4 are available at the National Center for Biotechnology Information (NCBI) under BioProject PRJNA1149023 (accession numbers JBHMQL000000000 , JBHMQK000000000 , and JBHLSP000000000 ).

    Techniques: Generated, Construct, Isolation, Comparison

    Genomic features of S. vaginalis isolates WSU1, WSU2, and WSU4

    Journal: Microbiology Resource Announcements

    Article Title: Draft genomes of three Sneathia vaginalis isolates from a patient with bacterial vaginosis

    doi: 10.1128/mra.00941-24

    Figure Lengend Snippet: Genomic features of S. vaginalis isolates WSU1, WSU2, and WSU4

    Article Snippet: The annotated draft genomes of Sneathia vaginalis isolates WSU1, WSU2, and WSU4 are available at the National Center for Biotechnology Information (NCBI) under BioProject PRJNA1149023 (accession numbers JBHMQL000000000 , JBHMQK000000000 , and JBHLSP000000000 ).

    Techniques: Sequencing