As many of our species' transcripts were derived from de novo assembled transcriptomes, there were a number of partial sequences that could bias alignments and phylogenetic analyses.
These biased alignments were generated by producing MUSCLE profile-profile alignments in a step-wise manner, assuming evolutionary relationships of the different domain subtypes that are contradictory to what the original trees suggest.
That said, each DO sample will have a unique set of SNPs and indels that can bias read alignment, and in total across a large population of DO mice, the number of alignment-sensitive genes will approach the sum of all genes that are sensitive to alignment bias across all of the eight founder strains.
To overcome a bias in alignment of short reads, where the reference allele reads are preferentially aligned over reads with the variant allele, we used a genomic reference containing IUPAC codes for SNPs in dbSNP.
Without correction, the missing wedge is the strongest feature in individual subtomograms and tends to bias the alignment of any two given subvolumes, favoring orientations with maximum density overlap as opposed to optimizing the overlap of matching structural features (Fig. 7).
Masking avoided bias in alignment between bisulfite modified and un-modified sequences.
Unlike the previous analysis [ 2], in order not to introduce subjective bias, manual alignment editing was minimized.
Either treatment abolished the bias in alignment and equalized the number of end-on attached unaligned kinetochores.
It was possible that the offset of representative TSSs between human and mouse could bias the alignment scores.
To not bias the alignment by the choice of a reference, each trajectory was separately used as a reference to which all the remaining trajectories were aligned.
