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With sequencing of complete genomes and development of comparative genomic methods, extensive analysis of a complex regulatory system in multiple genomes has become possible.
Previously, anchor identification among multiple genomes has been achieved using pairwise alignment tools like BLASTZ through progressive alignment tools like TBA, but the computational requirements for sequence comparisons of multiple genomes quickly becomes a limiting factor as the number and scale of genomes grows.
The prediction of functional linkage between the genes involved in several metabolic pathways across the multiple genomes has been demonstrated to correlate functional with physical linkages of gene clusters [ 25].
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As DNA-sequencing costs plummet, other biomedical projects analyzing multiple genomes have sprouted up, but Durbin believes the Wellcome Trust one is at the "top end of what people are doing".
Current models, based on global-level analyses of domain combinations in multiple genomes, have suggested that the propensity of some domains to associate with other domains in high-level architectures increases with organismal complexity.
The increasing availability of sequences and the now common need to align multiple whole genomes has repeatedly pushed each of these homology search algorithms to the point where they are no longer viable, demanding the development of software that takes advantage of new technologies and novel algorithms with refined heuristics.
Our recent survey of GATA genes from the whole-genome sequence of multiple protostome genomes has identified at least four GATA genes in every currently available protostome genome, with gene duplications having occurred only within the GATA456 class [ 6].
The sequencing of multiple plant genomes has dramatically improved our understanding of the impact of whole-genome duplication and transposable elements (TEs) on the organization of angiosperm genomes (Kejnovsky et al. 2009).
Scanning multiple related genomes has the added benefit of identifying polymorphic, putative, phase-variable loci that fail to meet the identification threshold in one strain but meet it in another.
The availability of multiple sequenced genomes has been very helpful in phylogenetic and functional studies of cyanobacterial genes, such as those in restriction-modification systems [ 21] and two-component systems [ 22].
The availability of multiple sequenced mammalian genomes has greatly increased possibilities for making broadly based, and therefore more accurate, identification of evolutionarily conserved features within the human genome.
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