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Transcripts arising from 16% of the selected CGs used conserved reading frames of translation from all the parent genes, thereby forming chimeric proteins by joining the domains of their respective parent genes (Table 1).
Alternatively, the CG transcript may be translated using the conserved reading frame from only one parent gene.
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Each sequence tag represents a number of sequence reads, thus sequence reads comprising the conserved tags are also regarded as conserved reads.
The total numbers of conserved reads from dissected seed parts at 4 stages are shown in Figure 2B.
To further explore the 5DS gene space, conserved read probes hybridizing to MTP clones were functionally assessed.
For conserved read probes, 1.34x coverage 454 Roche sequence reads derived from 5DS were blasted against related grass proteomes of Brachypodium distachyon, Oryza sativa and Sorghum bicolor.
Using these conserved reads, TR-GAG was estimated to range from 0 to 696.7 copies in diploid species and from 10.2 to 1,168.7 copies in C. arabica.
The secondary structure of the inverted repeat predicted by Mfold and evaluated by MirCheck showed that 6 conserved reads were found (Additional files 3, 4).
The 454 sequences (table 2) were first used to survey the presence of highly conserved reads of TR-GAG, using the criteria of 80% minimum nucleotide identity with over 80% of the read length.
Since these conserved reads cannot be assigned with any certainty to one specific genome, we distributed them to the respective candidate genomes in the proportion previously calculated from the unique reads.
Functional annotations of these conserved read probes gave insights into the gene space of 5DS (Fig. 9).
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