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Dot plot alignment of the CG14 and Nipponbare orthologous sequences around genes 88O22.2/88O22.7 evidenced a paracentric chromosomal inversion of approximately 45 kb (Figure 3, box D).
Figure S2 shows the dot plot alignment between contig JSAE01000257 and BACR26J21.
The dot plot alignment of the phages CP21 and CP220/CPt10 showed that their genomes are closely related but differently organized (Fig. 5b).
A dot plot alignment of the terminase gene products (TerL) confirmed our basic subcluster/cluster assignment with 100% of phages grouping by their pre-assigned subclusters and 90% by their clusters, while 12 of 15 singletons remaining singletons.
A dot plot alignment of these two clusters clearly showed a co-linear segment that reveals high nucleotide sequence conservation, and indicated homologies between all nsLtp genes mainly limited to the ORFs (data not shown).
A dot plot alignment of the terminase gene products (TerL) confirmed our basic cluster/subcluster assignment with 100% of phages grouping by their pre-assigned clusters or subclusters, and 11 of 14 singletons remaining singletons.
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The dot plot alignments were generated using the MUMmer package [37] (http://mummer.sourceforge.net/).net/
Further, note that two perfect dot plot alignments can still have different quality when analyzed with the FRC.
The potato-tomato dot plot alignments explained the discrepancies that were found between the potato and tomato genetic maps.
Dot plot alignments were generated using the EMBOSS dottup program (Rice et al. 2000) with window size = 9 and step size = 1.
Included in the refinement process were dot plot alignments of DM chromosome PM sequences to pre-release and finished versions of the tomato genome sequence (The Tomato Genome Sequencing Consortium 2012).
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