8.592J | Spring 2011 | Graduate

Statistical Physics in Biology


Problem Set 1 (PDF)

The .fna file below contains the nucleic acid sequence of E. coli in the FASTA format. A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. (FNA - 4.5 MB)

cSNPsAfricanEuropean (DAT)

cSNPsAfricanEuropeanType (DAT)

Problem Set 2 (PDF)

Altschul, S.F., et al. “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.” Nucleic Acids Res. 25, no. 17 (1997): 3389-402.

Problem Set 3 (PDF)  
Problem Set 4 (PDF)  
Problem Set 5 (PDF) 1TEN.PDB (PDB)

Miyazawa, Sanzo, and Robert L. Jernigan (MJ). “Residue–Residue Potentials with a Favorable Contact Pair Term and an Unfavorable High Packing Density Term, for Simulation and Threading.J. Mol Biol. 256, no. 3 (1996): 623-44.

MJ Interaction Table (3) (PDF)

Problem Set 6 (PDF)

The RNA Puller @ Ohio-State University

Smith, S.B., et al. “Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules.” Science 271 no. 5250 (1996): 795–9.

Problem Set 7 (PDF)  
Problem Set 8 (PDF) purR_sites (TXT)
gene_table (TXT)

Course Info

As Taught In
Spring 2011
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Problem Sets
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