Among the non-identical substitutions, the highest increase has been observed for the alignments of PB f (C cap β strand), PB k and l (loop to N cap α helix).
Importantly, disabling the seed resulted in an extra 0.9% of high-quality hits and identified a population of reads showing nucleotide misincorporation patterns characteristic of post-mortem damage and no reduction in read size, as would have been observed for spurious alignments.
No significant differences were observed for the alignment scores based on the reliable sequences, when sequences with discrepancies were included or excluded from the MSA.
For the heterogeneously distributed data that were observed for stem alignment and stem centralization, Wilcoxon signed rank test was used.
If (a) is often observed for an alignment program, efforts should be made to improve its underlying objective function.
A trend appears, from the greatest discrepancy observed for the shortest alignments, to an almost systematic agreement for the longest alignments.
As observed for SMR-BAT alignments, the SMR fusion 'N-terminus regions' (TM1 2 and TM5 6) showed the poorest TM domain alignments to N-terminus and central regions of DMT (TM1 2 and TM5 6) and MFS (TM1 3 and TM6 8) sequences.
In general, while a strong signal was observed for all the alignment-free methods on the low GC-content group, a weaker signal was observed on the moderate GC-content genomes (supplementary table S3, Supplementary Material online).
These results suggest that the depth-related bias observed for the single-round alignments was not due to biased consensus calling (since that would still affect the filtered analysis), but instead stems from differences in genomic coverage between low- and high-depth genomes.
However, the resulting fibers do not present the mutual alignment observed for nanofibers grown on mica [21].
