# Harvard:Biophysics 101/2007/02/01

Biophysics 101: Genomics, Computing, and Economics

Post comments/questions to the discussion page (the 2nd tab at the top)

## Tasks to complete by Feb 6

• Register an account on OWW
• Populate your user page with the following information
• Name
• Concentration
• Affiliation & Year
• Optional: anything else you wish to share (e.g. personal interests, photo, links)
• If anyone has problems with the following, the TFs will schedule meetings to provide individual walkthroughs.
• Once you have Python and BioPython installed, try running the following code
• This is done by copying and pasting the code into an empty text file and saving it on your machine.
• The code can be executed in a number of ways (described here)
• Also, look here and here for more information on getting started
```#!/usr/bin/env python

from Bio import GenBank, Seq

# We can create a GenBank object that will parse a raw record
# This facilitates extracting specific information from the sequences
record_parser = GenBank.FeatureParser()

# NCBIDictionary is an interface to Genbank
ncbi_dict = GenBank.NCBIDictionary('nucleotide', 'genbank', parser = record_parser)

# If you pass NCBIDictionary a GenBank id, it will download that record
parsed_record = ncbi_dict['116496646']

print "GenBank id:", parsed_record.id

# Extract the sequence from the parsed_record
s = parsed_record.seq.tostring()
print "total sequence length:", len(s)

max_repeat = 9

print "method 1"
for i in range(max_repeat):
substr = ''.join(['A' for n in range(i+1)])
print substr, s.count(substr)

print "\nmethod 2"
for i in range(max_repeat):
substr = ''.join(['A' for n in range(i+1)])
count = 0
pos = s.find(substr,0)
while not pos == -1:
count = count + 1
pos = s.find(substr,pos+1)
print substr, count
```
• Modify the code to do the following things
• Process a different GenBank ID of your choosing
• Tally stretches of poly-T instead of poly-A
• Print the translated protein sequence (hint) and its length
• Create a new NCBIDictionary without a parser and use that to print the a raw record (hint)
• Paste your code onto your user page when you are complete.