Depth of Conservation (May/20/2010)

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Presentation transcript:

Depth of Conservation (May/20/2010) Giltae Song, Bob Harris Penn State Center for Comparative Genomics and Bioinformatics gsong@bx.psu.edu, rsharris@bx.psu.edu

Our Question: Do different elements exhibit different conservation profiles?

Alignable Proportion Alignable Proportion = fraction of intervals that are at least half aligned

Alignable Proportion Measured for each human-vs-other alignment, Plotted at human-to-other distance

Alignable Proportion Unnormalized

Alignable Proportion Unnormalized Low Coverage Genomes

Alignable Proportion—Normalized Normalize by dividing by alignable proportion of coding exons

Alignable Proportion—Normalized Curve fit through “distant” high coverage assemblies (species names in black)

Alignable Proportion Envelopes

Alignable Proportion—Class 22

Alignable Proportion—Class 3

Alignable Proportion—Class 8

Alignable Proportion—Class 6

Similar measure for species/depth conservation of TFBS motifs Ongoing Similar measure for species/depth conservation of TFBS motifs More plots via http://www.bx.psu.edu/~rsharris/encode/index.html