This is an archived course. A more recent version may be available at ocw.mit.edu.

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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)
Problem Set 2 (PDF) Article by Altschul et al on BLAST
Problem Set 3 (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)
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." JMB. (PDF)

MJ Interaction Table (3) (PDF)
Problem Set 6 (PDF) The RNA Puller @ Ohio-State University
Problem Set 7 (PDF)  
Problem Set 8 (PDF) purR_sites.txt (TXT)
gene_table.txt (TXT)