Note: lifted from hg17
This track shows RNA secondary structure predictions made with the
EvoFold 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
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 elements of
an 8-way vertebrate alignment of the human, chimpanzee, mouse, rat,
dog, chicken, zebrafish, and Fugu assemblies. NOTE: These predictions
were originally computed on the hg17 (May 2004) human assembly, from
which the hg16 (July 2003), hg18 (May 2006), and hg19 (Feb 2009) predictions
were lifted. As a result, the multiple alignments shown on the track
details pages may differ from the 8-way alignments used for their
prediction. Additionally, some weak predictions have been eliminated
from the set displayed on hg18 and hg19. The hg17 prediction set corresponds
exactly to the set analyzed in the EvoFold paper referenced below.
The EvoFold program and browser track were developed by
Jakob Skou Pedersen
of the UCSC Genome Bioinformatics Group, now at
Aarhus University, Denmark.
The RNA secondary structure is rendered using the VARNA Java applet.
Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W,
Identification and classification of conserved RNA secondary structures in the human genome.
PLoS Comput Biol. 2006 Apr;2(4):e33.
PMID: 16628248; PMC: PMC1440920
Knudsen B, Hein J.
RNA secondary structure prediction using stochastic context-free grammars and evolutionary
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
Nucleic Acids Res. 2004;32(16):4925-36.
PMID: 15448187; PMC: PMC519121
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.
PMID: 16024819; PMC: PMC1182216