1. Journal club 06/27/08

2. Non-coding functional regions Cis-regulation of pre-mRNA splicing Post-splicing (mature mRNA) – degradation, localization Translational efficiency & accuracy – Choice of synonymous codon Secondary structure elements

3. CRUNCS Coding regions under non-coding selection Are not located in non-functional sequences as are, ex: most known transcription factors binding sites, but rather in coding regions

4. Mixture selective pressure Maintain the function of the protein encoded by the gene (AA selecvtive pressure) Maintain their regulatory role (CRUNCS) – ex: regulatory factors binding sites

5. Methods Sequence conservation: 1.Entropy score 2.Parsimony score Conservation p-value (mixture models) Posterior distributions of conservation scores Conditional p-values

7. Fitch’s algorithm