Lentiviruses exploit differential and alternative splicing, and overlapping reading frames to generate the proteins necessary for maintaining their life cycles [2], [4].
In the following discussion we use the terms "alternative pair" and "overlapping" in referring to relationships of D-domains.
For this analysis, the longest transcripts were selected and if alternative transcripts overlapped and extended the longest one, these extensions were annexed and this new pseudo-transcript was taken as the final model.
Our analysis identified 19, 280, and 538 genes containing alternative exons overlapping with predicted miRNA binding sites for the comparison of 4-/1-, 4+/1-, and 4+/1- tumors, respectively.
(2) The data was scanned for alternative splicing, and 6260 (30.5%) out of a total of 20514 sequences represent alternative splicing including some forward encoded alternative splicings overlapping with reverse encoded alternative splicings.
As an addition (or alternative) to overlapping spectra, we also propose an efficient dynamic programming algorithm for de novo peptide sequencing with accurate peptide masses and evaluate the resulting contribution to de novo sequencing accuracy.
Since reads generated from the alternative allele overlapping a differentiating site will have at least a single base mismatch to the reference genome, we successively allowed one (-v 1), two (-v 2), or three (-v 3) mismatches, but still required unique alignment to the reference genome (-m 1).
We need to improve the methods to obtain robust results, even when the alternative and null distributions overlap by so much.
An alternative, overlapping, way to capture the problem is to examine "promoter groups"—federations controlled by clans or individuals.
The primary transcript sequence of RAD9A exhibited two alternative, overlapping 5'ss at exon E8, identified as CAG/ G C A G /GT at the distal 5'ss and CAG/GTA GTT at the proximal 5'ss that extends E8 (non-consensus nucleotides are underlined; exon extension bolded).
