Journal club06/27/08
Non-coding functional regions
• Cis-regulation of pre-mRNA splicing• Post-splicing (mature mRNA) –
degradation, localization• Translational efficiency & accuracy –
Choice of synonymous codonSecondary structure elements
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
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
Methods
• Sequence conservation:1. Entropy score2. Parsimony score• Conservation p-value (mixture models)• Posterior distributions of conservation
scores• Conditional p-values
Fitch’s algorithm