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Such a complete genome analysis is only possible through re-sequencing, and in particular, through the next-generation sequencing technologies that make comparative genome sequencing feasible.
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Before proceeding in our quest for rules or organization, it is essential to make explicit a constraint that drives all living systems and makes comparative genome analyses difficult.
With the growing number of genome sequences, we can expect to get more sequences for obligate intracellular and free-living bacteria in all phyla, in order to make comparative genomic analyses including phyla remaining unstudied to date.
The increasing availability of multiple genome sequences has made comparative genomic analyses of P. aeruginosa possible.
The plummeting cost of genome sequencing is making comparative genomics an attractive technique, and creative bioinoformatic methods which take advantage of targeted sequencing are becoming more prevalent [ 14- 16].
In order to use whole genome information to make comparative analysis among genomes, we can use the first N components (M1, M2, …, M N ) of the moment vector of a genome sequence graph to represent a genome as a point in N-dimensional space.
Therefore, this genome space can be used to make comparative analysis to study the clustering and phylogenetic relationship among genomes.
The availability of several whole genome sequences makes comparative analyses possible.
As the entire genome sequence of P. falciparum is available and the macronuclear sequencing project of T. thermophila was just recently completed, we made comparative BLAST analyses against both genome sequences.
These next-generation linkage maps will facilitate the analysis of conifer genome evolution, by making comparative mapping possible at a scale that was not achievable with previous, low-throughput marker systems (for example, [ 37]).
Our comparison with other ORFeomes makes comparative analyses straighforward and facilitates direct comparisons of many proteins across many genomes.
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