MKAR Datasets
MKAR Test
- A variation of the McDonald-Kreitman test is used to examine intraspecific (human, personal genomes) polymorphism and interspecific (human-chimp and human-orangutan) divergence in noncoding DNA in non-overlapping 10kb windows slid across the human genome.
- [paper]
- software
MKAR Results
Data for all windows with sufficient counts for the MKAR test:
- Divergence reckoned with chimp, 10 personal genomes, sliding 10kb window pg10PanTro.txt.gz
- Divergence reckoned with orangutan, 10 personal genomes, sliding 10kb window pg10PonAbe.txt.gz
- View in local copy of the UCSC Genome Browser, PSU browser
Input Data
- Human polymorphism data:
- Personal genome SNPs that are public. Craig Venter, James Watson, YRI NA18507, YanHuang(YH) anonymous individual, Korean (SJK), CEU NA12891, NA12892, and YRI NA19240.
- Repeats ancestral to Orangutan:
- ARs, interspersed repeats ancestral to human and orangutan, defined as repeat elements that at least 70% aligns with orangutan (90% ID in gap free segments). These were filtered to remove elements shown to be evolving non-neutrally, or to have acquired functional regulatory roles
(ie MER121 and exapted repeats).
- Coding exons (for masking) are available from the
UCSC Table Browser
- We used UCSC Known Genes, coding exons only.
- Whole-genome alignments are available for bulk download from the UCSC Genome Browser
Miscellaneous
This work is a collaborative effort among researchers in Anthropology, Biology and the Center for Comparative Genomics and Bioinformatics at the Pennsylvania State University