User:Mdwang

Profile

Michael Wang
Biochemistry
Harvard College 2004-7
Genomics, Public Health, Informatics
Current Classes: Biophysics 101, Physics 11b, General Education 187

Assignments

Feburary 1

1. !/usr/bin/env python

from Bio.Seq import translate from Bio import GenBank, Seq import sys

1. user defines which array element to pick

array_position = int(sys.argv[-1]) print "Retrieving entry number ",array_position

1. Creates a non-parsed library of genes with search terms Xenopus and notch

search_terms = "Xenopus AND notch" gi_list = GenBank.search_for(search_terms) print "Searching for", search_terms, "entries" print gi_list print "Done searching" print "Entry ",array_position ncbi_dict_alpha = GenBank.NCBIDictionary('nucleotide', 'genbank')

1. prints the raw entry

print ncbi_dict_alpha[gi_list[0]]

1. We can create a GenBank object that will parse a raw record
2. This facilitates extracting specific information from the sequences

record_parser = GenBank.FeatureParser()

1. NCBIDictionary is an interface to Genbank

ncbi_dict = GenBank.NCBIDictionary('nucleotide', 'genbank', parser = record_parser)

1. If you pass NCBIDictionary a GenBank id, it will download that record

parsed_record = ncbi_dict[gi_list[0]] print parsed_record print "GenBank id:", parsed_record.id

1. Extract the sequence from the parsed_record

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

1. Translating the raw sequence

my_protein = translate(s) print "translated sequence:", my_protein

max_repeat = 9

print "multiple T analysis" print "method 1" for i in range(max_repeat):

   substr = .join(['T' for n in range(i+1)])
   print substr, s.count(substr)

print "\nmethod 2" for i in range(max_repeat):

   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