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If two or more sequences represented the same transcript they were assembled into a 'contig'contig
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We speculate that the more similar sequences represented as tips close (with few sequence differences) to their common ancestor are probably allelic differences at the same locus.
After removing adapters and low-quality sequences, the sequences represented more than 20× coverage of the genome (aligned bases divided by 950 Mbp length of the tomato genome).
Probes containing sequences represented more than once in the genome were omitted from the final array design, and all probes in the 'ultra-high density' probe sets were unique within the TAIR8 annotated reference genome.
We identified ten families of highly related aptamers that together cover more than 46% (33 aptamers) of all individual sequences obtained from the selection; one single individual sequence dominated the selection and constituted 8% of all the clones; five other sequences represented together more than 15% of the clones.
We estimated the sequencing redundancy at 39% based on the number of consensus sequences represented by more than one cDNA clone.
The proportion of consensus sequences represented by more than one cDNA clone was only 39%, which provides an estimate of the sequencing redundancy.
Overall, 298 transcripts with novel 5′ exons were identified, thus signifying novel transcription start sites (TSS), some of which are potentially germline specific, with 22 sequences represented by more than one novel exon.
All mature miRNA sequences represented by more than 3 reads within any of these datasets [ 39] were compared and transitively clustered into miRNA families defined through a pairwise Levenshtein distance ≤ 3. Directly using sequences rather than names allocated by authors avoids complications due to inconsistent naming conventions in the literature, of which we found several.
These were defined as those sequences represented by no more than 2 coding sequences from the CL-Brener (reference) genome in our sequence alignments (see below).
The 12 annotated α chain sequences recovered directly from genome database clearly represented fragments of genes, whereas the five β chain sequences represented a much more complete data set (Fig. 1A).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com