Divergence (K) is calculated as the number of substitution per site between the two duplication alignments.
Divergence is calculated as the number of substitution per site between the two duplication alignments.
To address this issue, we systematically examined predicted SNP alleles in segmental duplications and mutations inferred from duplication alignments.
A genome-wide set of 2,366 duplication alignments demonstrated the enrichment of Alu elements near the junction between the two duplicated sequences in all cases, suggesting Alu involvement in these rearrangements [ 40].
In BAC 604D2, six sequence contigs could be arranged through identification of target site duplications and alignment with reference transposon sequences whereas in BAC 509D2, a CACTA transposon was used to connect two large sequence contigs.
First, it reduces the cost of detecting false-positives as it filters out paralogs, with the exception of those caused by tandem gene duplication, and alignments to processed pseudogenes.
In this step, there are cases where, due to inserted bases in the sample that exactly repeat existing reference bases (short duplications), single alignments are rewritten as two overlapping read alignments, rather than simply divided in half, so that the single-alignment mapping results exactly match what would have been output in the two-alignment case.
The annotations of repetitive regions were downloaded from the UCSC genome browser, including transposons, microsatellites, simple tandem repeats, interrupted repeats, segmental duplications, self-alignment regions with similarity score > 80, and other repeats masked by RepeatMasker (http://www.repeatmasker.org).org
Additional file 5: Segmental duplication and gene alignment.
An approach to investigate the evolution of TPR domains in the subunits is to identify patterns of TPR duplication from the alignments.
