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About 0.2 and 0.2 %, respectively, of the unique sequences as known miRNAs were identified, which account for 4.1 and 3.3%%, respectively, of the total sRNAs.
Blast analysis identified 593 (56.3%) of the unique sequences as orthologs of genes from other organisms (E-value < 1e-5).
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All unique sequences as well as reference sequences have been accessioned in GenBank (see Additional files 1 and 2 for details).
The amount of unique sequence, as well as the total amounts of the genome sequence accounted for at each repeat copy-number, vary among the five strains indicating that the strains differ in their repeat structure and numbers of multicopy elements (Table 1).
The unique sequences considered as putative seabass pre-miRNAs were then searched against the miRBase database to predict conserved mature miRNAs in the Asian seabass (designated as lcal-miRNAs).
Finally 22.8% (8990) of the unique sequences were found only as transcripts.
Therefore, the unique sequences that were annotated as responsible for the formation of the SS backbones in the first two stages of the pathway were first screened.
We then performed a de novo transcriptome assembly on 10 million of the filtered reads with NGen, annotated full-length transcripts from contigs comprising ≥ 200 reads with significant blastx hits, and used the resulting unique sequences as a new filter.
All six of the proteins had "best-hits" in the same location of the genome as the unique sequences had, and visual inspection of alignments revealed premature stop codons were coded for in the Apis sequences in four out of the six cases.
The resulting set of the unique sequences with associated read counts was referred as sequence tags.
For AhLOX7 and AhPLD, the unique sequences obtained from amplicon sequencing were extracted as references.
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