Harvard:Biophysics 101/2007/Notebook:Resmi Charalel/2007-2-6

Assignment 1, due 2/6/07

Code for Assignment (This code performs all requested changes to original code):

#!/usr/bin/env python

from Bio import GenBank, Seq
from Bio.Seq import Seq,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
parsed_record = ncbi_dict['6273291']#Opuntia marenae rp16 gene; partial intron sequence

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(['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

start = s.find('ATG')
orf = 
c=start

for x in range(len(s)-start-4):
    orf = orf + s[c]
    c= c +1
    length = c-start
    remainder=length%3
    if remainder == 0:
        codon=s[c]+s[c+1]+s[c+2]
        if codon== 'TAA' or codon=='TAG' or codon=='TGA':
            orf=orf+s[c+1]+s[c+2]
            break

protein = translate(orf)

print 'protein sequence: ', protein
print 'protein length: ', len(protein)

rawdict = GenBank.NCBIDictionary('nucleotide', 'genbank')
rawrec = rawdict['6273291']
print "raw record: ", rawrec
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Output of Code:


GenBank id: AF191665.1
total sequence length: 902
method 1
T 279
TT 68
TTT 14
TTTT 7
TTTTT 4
TTTTTT 2
TTTTTTT 0
TTTTTTTT 0
TTTTTTTTT 0

method 2
T 279
TT 84
TTT 25
TTTT 13
TTTTT 6
TTTTTT 2
TTTTTTT 0
TTTTTTTT 0
TTTTTTTTT 0
protein sequence:  MRINGKAKERKK
protein length:  12
raw record:  LOCUS       AF191665                 902 bp    DNA     linear   PLN 07-NOV-1999
DEFINITION  Opuntia marenae rpl16 gene; chloroplast gene for chloroplast
            product, partial intron sequence.
ACCESSION   AF191665
VERSION     AF191665.1  GI:6273291
KEYWORDS    .
SOURCE      chloroplast Opuntia marenae
  ORGANISM  Opuntia marenae
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            Caryophyllales; Cactaceae; Opuntioideae; Opuntia.
REFERENCE   1  (bases 1 to 902)
  AUTHORS   Dickie,S.L. and Wallace,R.S.
  TITLE     Phylogeny of the subfamily Opuntioideae (Cactaceae)
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 902)
  AUTHORS   Dickie,S.L. and Wallace,R.S.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-SEP-1999) Botany, Iowa State University, 353 Bessey
            Hall, Ames, IA 50011-1020, USA
FEATURES             Location/Qualifiers
     source          1..902
                     /organism="Opuntia marenae"
                     /organelle="plastid:chloroplast"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:106980"
                     /note="subfamily Opuntioideae; synonym: Marenopuntia
                     marenae, Grusonia marenae"
     gene            <1..>902
                     /gene="rpl16"
     intron          <1..>902
                     /gene="rpl16"
ORIGIN      
        1 tatacattaa aggaggggga tgcggataaa tggaaaggcg aaagaaagaa aaaaatgaat
       61 ctaaatgata taggattcca ctatgtaagg tctttgaatc atatcataaa agacaatgta
      121 ataaagcatg aatacagatt cacacataat tatctgatat gaatctattc atagaaaaaa
      181 gaaaaaagta agagcctccg gccaataaag actaagaggg ttggctcaag aacaaagttc
      241 attaagagct ccattgtaga attcagacct aatcattaat caagaagcga tgggaacgat
      301 gtaatccatg aatacagaag attcaattga aaaagatcct atgntcattg gaaggatggc
      361 ggaacgaacc agagaccaat tcatctattc tgaaaagtga taaactaatc ctataaaact
      421 aaaatagata ttgaaagagt aaatattcgc ccgcgaaaat tcctttttta ttaaattgct
      481 catattttct tttagcaatg caatctaata aaatatatct atacaaaaaa acatagacaa
      541 actatatata tatatatata taatatattt caaattccct tatatatcca aatataaaaa
      601 tatctaataa attagatgaa tatcaaagaa tctattgatt tagtgtatta ttaaatgtat
      661 atattaattc aatattatta ttctattcat ttttattcat tttcaaattt ataatatatt
      721 aatctatata ttaatttaga attctattct aattcgaatt caatttttaa atattcatat
      781 tcaattaaaa ttgaaatttt ttcattcgcg aggagccgga tgagaagaaa ctctcatgtc
      841 cggttctgta gtagagatgg aattaagaaa aaaccatcaa ctataacccc aaaagaacca
      901 ga
//
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