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This was driven by a large positive loading of the first principal component by the Streptococcus phage Cp-1, which segregated Non-CF2, and negative loadings on the set of phage genomes shared by Non-CF1Asthma, Non-CF4Spouse and the CF metagenomes.
The observation that there are a fraction of genes found in bacterial genomes shared by all members of a species and a fraction present only in a subset of the population gave rise to the core genomic hypothesis [ 18].
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This left 1156 orthologous clusters in the core genome shared by the four Dmel Providencia species isolates.
It resulted in only 6%% of the pan-genome shared by all genomes (core genome) revealing far greater diversity than expected (Lukjancenko et al. 2010).
Comparison of the predicted gene content was performed to identify the core genome shared by strains and the variable accessory genome between strains.
The core genome shared by all eleven strains is composed of 1,882 genes, which make up about 31%50%% of the genome repertoire.
The observed pan-genome shared by the 15 strains consisted of 4,730, genes including 1,202 core genes, 1,388 dispensable genes and 2,040 unique genes.
There were 2374 S. suis orthologous gene clusters and 1211 unique genes, and the observed pan-genome shared by the 13 strains consisted of 3585 genes.
There are 26.2 Mb of the human genome shared by all four technologies; the majority of which falls in CCDS exonic regions.
Finally, by comparing the genomes of a variety of strains representing the different clades and biotypes, the set of genes in the V. vulnificus genome shared by all V. vulnificus strains can be identified.
We could generate genome alignments of more than 1.5 kb for 537 locally collinear blocks (65,8% of the core genome) shared by the 13 A. macleodii strains sequenced presently, including strains belonging to the surface clade.
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