However, NGS datasets are virtually always presented as lists of reads, with each element in a list specifying the position (chromosome and base pair) and orientation (positive or negative strand) of a read.
Interestingly, the candidate for the D. melanogaster MRP-RNA is on the negative strand of an intron in the Dmel_CG10365 gene [GenBank: AE014297], although the function of this gene is still unknown.
The negative strand of HCV RNA, a viral replication intermediate, has been detected in the brain and cerebrospinal fluid [10], [12].
We treat the gapped PWM as a model of binding sites on both the positive and negative strand of DNA.
This decomposition ignores the fact that a PWM is almost always applied to the positive and negative strand of DNA.
The original argument that central systems are not modular (that is, not modular in the Fodorian sense)—and with it, the motivation for the negative strand of the modest modularity thesis still stands.
On the negative strand of 89K, peptides encoded by 05SSU0944 and 05SSU0943 exhibit 27% and 41% amino acid sequence identity with the SalK and the SalR proteins of Streptococcus salivarius, respectively, forming a TCSTS belonging to the Nar/LuxR family.
Nevertheless, BSL6 siRNAs were more widely spread along the BSL6 genome, with some peaks, particularly in the negative strand of 200 to 250 nt and 600 to 660 nt (Figure S1B).
Another function of TU-1B might be the regulation of SAT2 gene expression, since it has been described that exon 1B overlaps with the 5'UTR sequence of the SAT2 gene [2], situated on the negative strand of the chromosome 17, and therefore SHBG and SAT2 genes would produce natural sense-antisense pair transcripts that overlap head to head.
A3G deaminates dC residues in the negative strand of the complementary DNA (cDNA), originating dU.
