Statistical Physics in Biology

Assignments

ASSIGNMENTS	RELATED FILES
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) 2EBN.PDB (PDB) 4HHB_A.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)