To address this issue, we used the presence of subgenome-specific SNPs to filter alignments to those known to have both At and Dt reads represented from each pair of varieties and thence to confidently call adjacent varietal SNPs within the co-aligned reads in a 100-bp sliding window.
Misalignments are automatically detected in rpd3 by separately realigning recombinant sequences with each of their identified parents (rpd3 uses clustalw to do this; Chenna et al., 2003) and comparing these pair-wise alignments to those of the corresponding sequence pairs in the full multiple sequence alignment.
Similar results were also found when the two sets of A genome markers (all of the markers with alignment to A genomes including those with multiple alignment to other genomes, and A genome-specific markers) were used to estimate genetic distance for the three species.
This implies that for those terms alignment to VCM might require more work, more detailed icons (with more primitives) and therefore be more prone to coder errors, show lower levels of concordance, similarity and, finally, validity.
Any error-containing contigs - those without perfect alignments to the reference - were removed from consideration at this stage.
We investigated the PhyloP evolutionary conservation scores [ 32] applied to 28– and 44 species alignments, and to those alignments restricted to the placental mammals and human, for their ability to predict the disease association status of common variants.
The realigned beams pass through a filter that permits only those beams with a particular alignment to pass.
The woven cross-pattern displayed a simple alignment to investigate cell interactions, whereas more complex structures may conceal those processes.
Genome alignment methods often define their target alignment to consist of homologous nucleotides falling into one or more of those classes.
We parsed peptide alignments to count those with 100% identity and 100% alignment coverage (Additional file 2).
