In this article, we introduce a generalization of the transcriptome to genome spliced alignment problem, which allows the detection of transcriptional aberrations such as duplications, rearrangements and inversions.
In the past decade, a novel hepatitis B spliced protein (HBSP) encoded by a 2.2 kb singly spliced defective HBV genome (spliced between positions 2447 nt and 489 nt) has been detected in the liver tissues and the serum from patients with hepatitis B [ 9, 10].
This data demonstrates that the integrations in the genome are invariant in all single cells, whereas the HPV-to-genome splicing events differed between individual cells.
Also in comparison with gene sets in MSigDB, as well as with the full genome, the splicing factor gene set (and other splicing-related gene sets included in MSigDB) had a strong shift towards negative correlation in the same seven cancer datasets (Additional file 1: Figure S12).
It is estimated that approximately 60% of disease mutations in the human genome are splicing mutations [12], [13].
We calculated the correlations between genome and splicing quantities.
Peng et al. showed that during the generation of infection, putative 12-bp introns were inserted into protein-coding genes in an archaeal virus genome, although splicing was not demonstrated and the mechanism of insertion of the 12-bp sequence is unknown [ 39].
A human exon was assumed to be conserved in the mouse or dog genome if spliced alignment of the genomic fragment containing this exon and adjacent exons on both sides yielded exactly the same exon triple.
For all three genomes, alternative splicing was handled simply by renaming each alternative spliced transcript as "XXX_splic1", "XXX_splic2", etc.
The representative protein sequences were mapped to G. soja W05 genome using splice-site-aware aligner Exonerate52 (version 2.4.0) with the following parameters: –model protein2genome showalignment showtargetgff refine region.
