A summary of the data can be found in Table 2. Following alignment and quality assessment of the data, 23398 and 23701 variants were identified in exome data for VI-2 and VII-6, respectively.
This discrepancy is likely due to differences in the stringency of read alignment and quality control cutoffs, as all of the breseq indel and SNV predictions appeared to be high quality upon manual examination.
Alignments were combined under t-coffee, and quality of alignment assessed.
Finally, a score is assigned to each junction, dependent only on the strength of the alignment and the number and quality of bases supporting the splice junction.
The objective function is specifically tuned to finding SV events by taking into account the length and quality of alignments, the number of alignments in the OCS and the genomic distance between those alignments.
Sequence alignment and quality was analyzed with the use of Geneious software (Kearse et al. 2012).
A common region of alignment with respect to the translated ORF was found for the DNA sequences and the corresponding proteins based on length and quality of alignment criteria.
This choice was based on the image quality (no preparation artifacts), degree of symmetry and quality of alignment.
(B ) Alignment of yeast and human StART-like domains with Bet-v1 and seven human StARTs, with CLUSTALX coloring of conserved residues, together with secondary structure (above, sheets blue arrows, helices red) and quality of alignment (below).
