6

Announcements: problem set due new problem set Finish ch. 6 Start ch. 7

DNA->RNA->Protein

Codon Usage

Using statistics

• find all long ORFs (>50 bps)
• codon usage divergence in ORF
• set a threshold or prioritize on score

divergence: q log q - q log p

Eukaryotic splicing

How splicing happens

Spliceosome

Intron discarded

Basic intron/exon structure

Profile

Statistical methods on Eukaryotes

Exon Chaining

Similarity based gene searching/structuring

Amino acid to DNA alignment

Approaches range unprincipled:3-frame translation of DNA followed by protein alignment principled:intermediate `iDNA' sequence aligned to both DNA and protein, sum scores semi-principled:limit the inserts in DNA relative to iDNA

DNA: AGT GTA G-T GCC -CT CTAG TTCA iDNA: AGT GTA GAT GCC CCT -TAG -TGA iAA: T V G A P X S AA: T V S - P G S

Spliced alignment problem