Most of these Transcriptional Units in both human and mouse present conserved sizeable sequences (>40 bp) overlapping Hox transcripts, suggesting that these Hox antisense transcripts are functional.
Standard DNA sequencing of sizeable gene regions in large study populations with the aim to identify the contribution of rare mutation is time-consuming and cost-intensive.
We found that 5.5% of the D. albomicans genome consists of repetitive elements (compared to 5.35% of D. melanogaster [ 21], Additional File 4), suggesting that our short-read assembly has captured a sizeable fraction of repeat sequences.
Despite this, a sizeable fraction of 5' UTR sequences have no uORFs at all, including some of those above 400 nt in length when at least three uORFs are expected by chance (see Additional File 2).
However, most of these investigations have focused on microsatellites with sizeable repeat numbers, leaving sequences with small repeat numbers largely unexplored (Zhu et al. 2000; Noor et al. 2001; Dieringer and Schlötterer 2003; Ellegren 2004).
Problematic placements included B. mori, where the predicted sequences contained sizeable gaps (Additional file 14), which could in part be due to the quality of the genome, as we indicated for our prediction of the B. mori Dscam-hv gene (Additional file 2).
Furthermore, there was a sizeable gap in the predicted sequence of T. castaneum Dscam3 (Additional file 14), the placement of which also does not match the evolutionary relationships among the organisms.
This observation led to the hypothesis that, along with SLSs stochastically formed because of sequence composition, a sizeable quota is possibly the result of selective pressure, due to the need to preserve a biological function.
Data sets that had a sizeable contribution (>30) of both IGSP sequences and non-IGSP sequences were aligned with MUSCLE v3.6 [45] and analyzed for recombination signals using the 3SEQ algorithm [33], [46].
For this reason, sizeable portions of the other predicted sequences were expected to yield many useful gRNA predictions.
