Harvard:Biophysics 101/2007/02/01
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Tasks to complete by Feb 6
- Register an account on OWW
- See this page for instructions
- Populate your user page with the following information
- Name
- Concentration
- Affiliation & Year
- Research/academic interests
- Optional: anything else you wish to share (e.g. personal interests, photo, links)
- Link to your userpage from our People page
- If anyone has problems with the following, the TFs will schedule meetings to provide individual walkthroughs.
- Download and install Python and BioPython (details here)
- Once you have Python and BioPython installed, try running the following code
#!/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
- Paste your code onto your user page when you are complete.