## Description

This track shows a measure of evolutionary conservation in seven species of the genus Saccharomyces based on a phylogenetic hidden Markov model (phastCons). The graphic display shows the alignment projected onto S. cerevisiae.

The genomes were downloaded from:

- S. cerevisiae - ftp://genome-ftp.stanford.edu/pub/yeast/data_download/sequence/genomic_sequence
- S. paradoxus - http://www.broad.mit.edu/ftp/pub/annotation/fungi/comp_yeasts/S1a.Assembly/Spar_contigs.fasta
- S. mikatae - http://www-genome.wi.mit.edu/ftp/pub/annotation/fungi/comp_yeasts/S1a.Assembly/Smik_contigs.fasta
- S. kudriavzevii - http://www.genetics.wustl.edu/saccharomycesgenomes/Contigs/YM6553.fsa.gz
- S. bayanus - http://www-genome.wi.mit.edu/ftp/pub/annotation/fungi/comp_yeasts/S1a.Assembly/Sbay_contigs.fasta
- S. castelli - http://www.genetics.wustl.edu/saccharomycesgenomes/Contigs/YM476.fsa.gz
- S. kluyveri - http://www.genetics.wustl.edu/saccharomycesgenomes/Contigs/YM479.fsa.gz

## Display Conventions and Configuration

In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.

Pairwise alignments of each species to the $organism genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons.

Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Configuration buttons are available to select all of the species (Set all), deselect all of the species (Clear all), or use the default settings (Set defaults). Note that excluding species from the pairwise display does not alter the the conservation score display.

To view detailed information about the alignments at a specific position, zoom the display in to 30,000 bases or fewer, then click on the alignment.

### Gap Annotation

The Display chains between alignments configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used:

- Single line: no bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the $organism genome or a lineage-specific deletion between the aligned blocks in the aligning species.
- Double line: aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species.
- Pale yellow coloring: aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species.

Downloads for data in this track are available:

- Multiz alignments (MAF format), and phylogenetic trees
- PhastCons conservation (WIG format)

### Base Level

When zoomed-in to the base-level display, the track shows the base composition of each alignment, with bases in annotated repetitive elements displayed in lower case. The numbers and symbols on the Gaps line indicate the lengths of gaps in the $organism sequence at those alignment positions relative to the longest non-$organism sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+".

Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes:

- No codon translation: the gene annotation is not used; the bases are displayed without translation.
- Use default species reading frames for translation: the annotations from the genome displayed in the Default species for translation; pull-down menu are used to translate all the aligned species present in the alignment.
- Use reading frames for species if available, otherwise no translation: codon translation is performed only for those species where the region is annotated as protein coding.
- Use reading frames for species if available, otherwise use default species: codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation.

Codon translation uses the following gene tracks as the basis for translation, depending on the species chosen (Table 2). Species listed in the row labeled "None" do not have species-specific reading frames for gene translation.

> Gene Track | Species
> SGD Genes | S. cerevisae
> No annotation | all the other yeast strains

> Table 2. Gene tracks used for codon translation.

## Methods

Best-in-genome pairwise alignments were generated for each species using blastz, followed by chaining and netting. The pairwise alignments were then multiply aligned using multiz, and the resulting multiple alignments were 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.
- AxtBest, axtChain, chainNet, netSyntenic, and netClass by Jim Kent at UCSC.
- PhastCons by Adam Siepel at Cornell University.
- "Wiggle track" plotting software by Hiram Clawson at UCSC.

## References

### Phylo-HMMs and phastCons:

Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104.

Siepel A, 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 JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50.

Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993-1005.

### Chain/Net:

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.

### Multiz:

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15.

### Blastz:

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26.