## Description

This track shows a measure of evolutionary conservation in $organism, chimp, mouse and rat based on a phylogenetic hidden Markov model (phastCons). Multiz alignments of the following assemblies were used to generate this annotation:

- $organism $date 003 ($db)
- chimp Nov. 2003 (panTro1)
- mouse Feb. 2003 (mm3) draft assembly
- rat Jun. 2003 (rn3)

## Methods

Multiz is a multiple alignment program that takes blastz "Best-in-Genome" alignments (axtBest or axtNet) as input. For $organism/rodent alignments, it uses the same scoring matrix as blastz between pairs of sequences:

            A     C     G     T
      A    91  -114   -31  -123
      C  -114   100  -125   -31
      G   -31  -125   100  -114
      T  -123   -31  -114    91

      O = 400, E = 30, K = 3000, L = 3000, M = 50

For the mouse/rat alignments the following matrix was used:

            A     C     G     T
      A    86  -135   -68  -157
      C  -135   100  -148   -68
      G   -68  -148   100  -135
      T  -157   -68  -135    86

      O = 600, E = 50

For the $organism/chimpanzee alignments the following matrix was used:

           A    C    G    T
     A   100 -300 -150 -300
     C  -300  100 -300 -150
     G  -150 -300  100 -300
     T  -300 -150 -300  100

     O = 400, E = 30, K = 4500, L = 4500, M = 50

The overall score is the sum of the score over all pairs.

The resulting $organism-chimp-mouse-rat multiple alignments were then assigned conservation scores by phastCons. The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Note that, unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size, so short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. (2005).

PhastCons currently treats alignment gaps as missing data, which sometimes has the effect of producing undesirably high conservation scores in gappy regions of the alignment. We are looking at several possible ways of improving the handling of alignment gaps.

## Credits

This track was created at UCSC using the following programs:

- Blastz and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group.
- Mouse sequence data are provided by the Mouse Genome Sequencing Consortium.
- Rat sequence data are provided by the Rat Sequencing Consortium.
- Chimpanzee sequence data are provided by the Chimpanzee Sequencing Consortium.
- Jim Kent wrote axtBest and the scripts to run multiz genome-wide and to display the alignments in this browser.
- PhastCons by Adam Siepel at Cornell University.
- "Wiggle track" plotting software by Hiram Clawson at UCSC.

## References

### Phylo-HMMs and phastCons

Felsenstein, J. and Churchill, G.A. A hidden Markov model approach to variation among sites in rate of evolution. Mol Biol Evol 13, 93-104 (1996).

Siepel, A. and Haussler, D. Phylogenetic hidden Markov models. In R. Nielsen, ed., Statistical Methods in Molecular Evolution, pp. 325-351, Springer, New York (2005).

Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S., Weinstock, G.M., Wilson, R. K., Gibbs, R.A., Kent, W.J., Miller, W., and Haussler, D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).

Yang, Z. A space-time process model for the evolution of DNA sequences. Genetics, 139, 993-1005 (1995).

### Chain/Net:

Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).

### Multiz:

Blanchette, M., Kent, W.J., Riemer, C., Elnitski, .L, Smit, A.F.A., Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D., Haussler, D., Miller, W. Aligning Multiple Genomic Sequences with the Threaded Blockset Aligner. Genome Res. 14(4), 708-15 (2004).

### Blastz:

Chiaromonte, F., Yap, V.B., and Miller, W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput 2002, 115-26 (2002).

Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., Haussler, D., and Miller, W. Human-Mouse Alignments with BLASTZ. Genome Res. 13(1), 103-7 (2003).