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This is the first report of sg DNAs for MSV and, to our knowledge, the first time that encapsidated sg DNAs have been characterized at the sequence level for any geminivirus.
In wheat, the TBP method produces species-specific amplification products, which can be either directly used as new DNA molecular markers capable of discriminating between T. aestivum and Triticum durum or analyzed at the sequence level for the design of species-specific probes.
Our findings at the DNA sequence level for these variants are consistent to those reported previously [9], [10].
Therefore, this approach is likely to help researchers to develop testable hypotheses about a protein's function even if is somewhat distant from the more characterized proteins, by facilitating the discovery of features that are conserved above the sequence level for comparison and further experimental investigation.
The irrE mutants obtained in this study were sequenced, and the mutations are summarized at both the primary sequence level (for all mutations), and at the homology model level (for mutations within the range of residues 44 303), shown in Figure 9A and Figure 9B.
There was no evidence of accelerated evolution at the sequence level for hsp genes.
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These sequences were found to be expressed in all strains and be entirely conserved at the sequence level except for one synonymous SNP in GA1 for the Proline racemase gene.
Genomics science facilitates characterization of entire eukaryote genomes at the DNA sequence level, but for crop plants with complex genomes such as sugarcane, gene characterization is currently best achieved via expressed sequence tag (EST) analysis where sequence information is restricted to genes that are actually functioning in a particular tissue or situation.
In summary, the results we report provide the sequence level basis for control of alx1 spatial expression by the double negative gate GRN architecture, and explain the rising, then falling temporal expression profile of the alx1 gene in terms of its auto-regulatory genetic wiring.
Our method does not require sequencing across CNV breakpoints (as paired-end methods do), but leverages sequence level data for exact CNV characterization where breakpoints are within targeted regions.
These data can then be used to investigate adaptation at the sequence level by, for example, detecting protein domains, individual codon sites or branches under positive selection (1); or developing resources for molecular evolutionary studies (2).
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