Harvard:Biophysics 101/2007/Notebook:Katie Fifer/2007-2-6

# Added translate so that we can use it in finding the protein translation from Bio import GenBank, Seq from Bio.Seq import translate # 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 # PART 1: A different GenBank ID parsed_record = ncbi_dict['116496513'] 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): # PART 2: Change A to T     substr = ''.join(['T' for n in range(i+1)]) print substr, s.count(substr) print "\nmethod 2" for i in range(max_repeat): # PART 2: Change A to T     substr = ''.join(['T' 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 # PART 3: Print the translated protein sequence print "protein translation is:" my_protein = translate(s) print my_protein print "its length is:", len(my_protein) # PART 4: New dictionary without parser. Just print raw record. ncbi_dict2 = GenBank.NCBIDictionary('nucleotide', 'genbank') new_raw_record = ncbi_dict2['116496513'] print '\n' print new_raw_record
 * 1) !/usr/bin/env python