## Description

This track shows RNA secondary structure predictions made with the EvoFold (v.2) program, a comparative method that exploits the evolutionary signal of genomic multiple-sequence alignments for identifying conserved functional RNA structures.

## Display Conventions and Configuration

Track elements are labeled using the convention ID_strand_score. When zoomed out beyond the base level, secondary structure prediction regions are indicated by blocks, with the stem-pairing regions shown in a darker shade than unpaired regions. Arrows indicate the predicted strand. When zoomed in to the base level, the specific secondary structure predictions are shown in parenthesis format. The confidence score for each position is indicated in grayscale, with darker shades corresponding to higher scores.

The details page for each track element shows the predicted secondary structure (labeled SS anno), together with details of the multiple species alignments at that location. Substitutions relative to the human sequence are color-coded according to their compatibility with the predicted secondary structure (see the color legend on the details page). Each prediction is assigned an overall score and a sequence of position-specific scores. The overall score measures evidence for any functional RNA structures in the given region, while the position-specific scores (0 - 9) measure the confidence of the base-specific annotations. Base-pairing positions are annotated with the same pair symbol. The offsets are provided to ease visual navigation of the alignment in terms of the human sequence. The offset is calculated (in units of ten) from the start position of the element on the positive strand or from the end position when on the negative strand.

The graphical display may be filtered to show only those track elements with scores that meet or exceed a certain threshhold. To set a threshhold, type the minimum score into the text box at the top of the description page.

## Methods

Evofold makes use of phylogenetic stochastic context-free grammars (phylo-SCFGs), which are combined probabilistic models of RNA secondary structure and primary sequence evolution. The predictions consist of both a specific RNA secondary structure and an overall score. The overall score is essentially a log-odd score between a phylo-SCFG modeling the constrained evolution of stem-pairing regions and one which only models unpaired regions.

The predictions for this track were based on the conserved segments of a human-referenced (hg18) 31-way vertebrate alignment comprising 28 mammalian assemblies and three other vertebrate assemblies (see Parker et al for details). The 31-way alignment is a subset of the 44-way alignment displayed on hg18.

## Additional resources

Auxiliary data sets and a family classification of the predictions can be browsed on a mirror site from here.

## Credits

The EvoFold program and browser track were developed by Jakob Skou Pedersen initially at UCSC Genome Bioinformatics Group and later at University of Copenhagen and at Aarhus University, Denmark (current position). Parker et al. describes the current set of predictions and their family classification. The multiple alignments used for the analysis were generated at UCSC as part of the 29 Mammals Sequencing and Analysis Consortium (Lindblad-Toh et al.).

The RNA secondary structure is rendered using the VARNA Java applet.

## References

### EvoFold

Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R, and Pedersen JS. New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Res. in press.

Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol. 2006 Apr;2(4):e33.

### Phylo-SCFGs

Knudsen B, Hein J. RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics. 1999 Jun;15(6):446-54.

Pedersen JS, Meyer IM, Forsberg R, Simmonds P, Hein J. A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res. 2004 Sep 24;32(16):4925-36.

### Alignments and conserved elements

Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, et al. A high-resolution map of evolutionary constraint in the human genome based on 29 eutherian mammals. In review.

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50.