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Exact(5)
The short read sequences often match to multiple loci of the genome.
In the second case, RM annotations include only the closest sequences known, and one sequence could easily match to multiple TE families.
For instance, in H. sapiens, 20% of the intergenic reads match to multiple locations in the genome, of which 6% match to 2 10 locations and 14% to more than 10 locations [ 31].
Uniquely matched tags to the sense strand of genes were included in this analysis and the distance for the longest splice variant was taken into consideration for tags that match to multiple splice variants of a gene.
Then, the nodes are classified into four categories: false negatives (ground-truth nodes without any match to the participant nodes), false positives (participant nodes without any match to the ground-truth nodes), true positives (ground-truth nodes that match to some participant nodes) and non-split nodes (participant nodes that match to multiple ground-truth nodes).
Similar(55)
The reads that matched to multiple genomic positions were discarded.
Tags matching to multiple genomic loci were discarded.
Markers with multiple matches to multiple chromosomes (or no chromosome matches) were not assigned to a chromosome.
The remaining 2.18% for delayed implantation and 2.24% for activation matched to multiple genes (Table 8).
An additional 1,673 probes were found to have dubious gene assignments (due, for example, to identical matches to multiple genes).
Blast matches to multiple loci, with the same top e-value were all selected for further interrogation.
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