These tracks show conservation scores and single-base-pair resolution significantly conserved or accelerated elements among three different alignments. The alignments used are:
We generated site-by-site conservation scores using phyloP(Pollard et al. 2010) with the --method LRT and --mode CONACC options. These scores were then corrected for multiple-testing using the BH FDR-controlling method(Benjamini and Hochberg 1995). Any site with a resulting q-value of less than 0.05 (for a <5% expected FDR) was deemed significantly conserved or accelerated.
PhyloP requires a neutral model to generate its scores. Our neutral model was generated based on neutrally-evolving ancestral repeats using phyloFit (from the PHAST(Hubisz, Pollard, and Siepel 2011) package) and the REV model, fit using the EM strategy. We then scaled this model to fit ancestral repeats from three different chromosome sets: macro-, micro-, and sex chromosomes. The resulting three neutral models were used to infer the final scores: when scoring the bases on each chromosome, the corresponding model was used for phyloP.
| Alignment | Macro-chromosome model | Micro-chromosome model | Sex chromosome model |
|---|---|---|---|
| 363-way | Macro model | Micro model | Sex model |
| 77-way | Macro model | Micro model | Sex model |
| 53-way | Macro model | Micro model | Sex model |
Both the 77-way and the 53-way scores were originally referenced on the galGal6 assembly. These were lifted over to galGal4 to be displayed on this browser, losing around 1% of the scores in the process.
The Bird 10K consortium, as well as the UCSC Genome Browser, provided the input data.
Please contact Joel Armstrong or the corresponding authors Guojie Zhang or Benedict Paten with questions.
Benjamini, Yoav, and Yosef Hochberg. 1995. “Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing.” Journal of the Royal Statistical Society. Series B (Methodological) 57 (1): 289–300. http://www.jstor.org/stable/2346101.
Blanchette, Mathieu, W. James Kent, Cathy Riemer, Laura Elnitski, Arian F A Smith, Krishna M. Roskin, Robert Baertsch, et al. 2004. “Aligning multiple genomic sequences with the threaded blockset aligner.” Genome Research 14 (4): 708–15. https://doi.org/10.1101/gr.1933104.
Hubisz, Melissa J., Katherine S. Pollard, and Adam Siepel. 2011. “PHAST and RPHAST: Phylogenetic analysis with space/time models.” Briefings in Bioinformatics 12 (1): 41–51. https://doi.org/10.1093/bib/bbq072.
Pollard, K. S., M. J. Hubisz, K. R. Rosenbloom, and A. Siepel. 2010. “Detection of nonneutral substitution rates on mammalian phylogenies.” Genome Res. 20 (1): 110–21.