Suggested Reading

Mount, Chapter 1, 2.

Molecular biology and information transfer

See Doug Brutlag's lecture.

Introduction to Macromolecular structures from Biochem503

Primer on molecular biology and the Genome Project

Computational Biology Problems

Very simple problems (solved for 20+ years).

• Finding restriction sites (regular expression pattern search)

• Translating DNA to protein (translation using genetic code)

• Alignment of two protein or DNA sequences

Algorithmically simple, but sometimes computationally demanding:

• DNA and protein sequence similarity searching - compare a protein sequence against 1000 - 100,000+ sequences.

• RNA folding

Difficult problems that are understood:

• DNA sequence fragment assembly - from sequence reads to physical maps

• Restriction mapping from single/double digestion data

• Evolutionary tree construction

Unsolved problems (that nature has solved):

• Protein secondary structure prediction

• Eukaryotic promoter site identification

• Identification of functional regulatory sites in eukaryotes

• Processing of splicesosomal introns - Gene recognition

• Protein folding

Problems that may not be solved by nature:

• From structure to function

• Integration of regulatory systems -- physiology.

wrp@virginia.edu