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 codon

Secondary 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 score

2. Parsimony score

• Conservation p-value (mixture models)

• Posterior distributions of conservation scores

• Conditional p-values

Fitch’s algorithm