User talk:Yanjia Jason Zhang

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Assignment #2

Exponential Curve

Python Code:

   import numpy as np
   import matplotlib.pyplot as plt
   a,b,c,d,k=1,1,[0],[0],0.8
   while a < 100:
       c.insert(len(c),a)
       d.insert(len(c),b)
       a=a+1
       b=b*k
   print c
   print d
   plt.plot(c,d,'bo')
   plt.show()

If anyone has comments, especially tips on how to make multiple curves on the matplot platform, I'd love to hear them! I have not programmed in more than a decade, so any comments are more than welcome.

Python Graphs: 1.) k=0.9

Image:Exponential_1_Py.png

2.) k=1.1

Image:Exponential_2_Py.png

Excel Graphs:

Image:Jason_excel_exp.png Notes:

  • when k<1, the curve is negatively sloped
  • when k>1, the curve is positively sloped
  • any small change in k gets amplified greatly

Assignment #3

Biophysics 101, Fall 2009

Assignment 3

PROBLEM #1

CODE:


p53='cggagcagctcactattcacccgatgagaggggaggagagagagagaaaatgtcctttag\
gccggttcctcttacttggcagagggaggctgctattctccgcctgcatttctttttctg\
gattacttagttatggcctttgcaaaggcaggggtatttgttttgatgcaaacctcaatc\
cctccccttctttgaatggtgtgccccaccccccgggtcgcctgcaacctaggcggacgc\
taccatggcgtagacagggagggaaagaagtgtgcagaaggcaagcccggaggcactttc\
aagaatgagcatatctcatcttcccggagaaaaaaaaaaaagaatggtacgtctgagaat\
gaaattttgaaagagtgcaatgatgggtcgtttgataatttgtcgggaaaaacaatctac\
ctgttatctagctttgggctaggccattccagttccagacgcaggctgaacgtcgtgaag\
cggaaggggcgggcccgcaggcgtccgtgtggtcctccgtgcagccctcggcccgagccg\
gttcttcctggtaggaggcggaactcgaattcatttctcccgctgccccatctcttagct\
cgcggttgtttcattccgcagtttcttcccatgcacctgccgcgtaccggccactttgtg\
ccgtacttacgtcatctttttcctaaatcgaggtggcatttacacacagcgccagtgcac\
acagcaagtgcacaggaagatgagttttggcccctaaccgctccgtgatgcctaccaagt\
cacagacccttttcatcgtcccagaaacgtttcatcacgtctcttcccagtcgattcccg\
accccacctttattttgatctccataaccattttgcctgttggagaacttcatatagaat\
ggaatcaggatgggcgctgtggctcacgcctgcactttggctcacgcctgcactttggga\
ggccgaggcgggcggattacttgaggataggagttccagaccagcgtggccaacgtggtg'

print 'Total number of cytosines:'
print p53.count('c')
print 'Total number of guanines:'
print p53.count('g') 
print 'Total number of Gs and Cs:'
print p53.count('c') + p53.count('g')
print 'Total Length of sequence'
print len(p53)
print 'GC content (as percentage)'
print 100.0*(p53.count('c')+p53.count('g'))/len(p53)

OUTPUT:


Total number of cytosines:
272

Total number of guanines:
268

Total number of Gs and Cs:
540

Total Length of sequence
1020

GC content (as percentage)
52.9411764706

PROBLEM #2

CODE:


p53='cggagcagctcactattcacccgatgagaggggaggagagagagagaaaatgtcctttag\
gccggttcctcttacttggcagagggaggctgctattctccgcctgcatttctttttctg\
gattacttagttatggcctttgcaaaggcaggggtatttgttttgatgcaaacctcaatc\
cctccccttctttgaatggtgtgccccaccccccgggtcgcctgcaacctaggcggacgc\
taccatggcgtagacagggagggaaagaagtgtgcagaaggcaagcccggaggcactttc\
aagaatgagcatatctcatcttcccggagaaaaaaaaaaaagaatggtacgtctgagaat\
gaaattttgaaagagtgcaatgatgggtcgtttgataatttgtcgggaaaaacaatctac\
ctgttatctagctttgggctaggccattccagttccagacgcaggctgaacgtcgtgaag\
cggaaggggcgggcccgcaggcgtccgtgtggtcctccgtgcagccctcggcccgagccg\
gttcttcctggtaggaggcggaactcgaattcatttctcccgctgccccatctcttagct\
cgcggttgtttcattccgcagtttcttcccatgcacctgccgcgtaccggccactttgtg\
ccgtacttacgtcatctttttcctaaatcgaggtggcatttacacacagcgccagtgcac\
acagcaagtgcacaggaagatgagttttggcccctaaccgctccgtgatgcctaccaagt\
cacagacccttttcatcgtcccagaaacgtttcatcacgtctcttcccagtcgattcccg\
accccacctttattttgatctccataaccattttgcctgttggagaacttcatatagaat\
ggaatcaggatgggcgctgtggctcacgcctgcactttggctcacgcctgcactttggga\
ggccgaggcgggcggattacttgaggataggagttccagaccagcgtggccaacgtggtg'

p53=p53.replace('a','T')
p53=p53.replace('t','a')
p53=p53.replace('c','G')
p53=p53.replace('g','c')
p53=p53.lower()
p53=p53[::-1]
print p53

OUTPUT:


caccacgttggccacgctggtctggaactcctatcctcaagtaatccgcccgcctcggcctcccaaagtgcaggcgtgagccaaagtgcaggcgtgagccacagcgcccatcctgattccattctatatgaagttctccaacaggcaaaatggttatggagatcaaaataaaggtggggtcgggaatcgactgggaagagacgtgatgaaacgtttctgggacgatgaaaagggtctgtgacttggtaggcatcacggagcggttaggggccaaaactcatcttcctgtgcacttgctgtgtgcactggcgctgtgtgtaaatgccacctcgatttaggaaaaagatgacgtaagtacggcacaaagtggccggtacgcggcaggtgcatgggaagaaactgcggaatgaaacaaccgcgagctaagagatggggcagcgggagaaatgaattcgagttccgcctcctaccaggaagaaccggctcgggccgagggctgcacggaggaccacacggacgcctgcgggcccgccccttccgcttcacgacgttcagcctgcgtctggaactggaatggcctagcccaaagctagataacaggtagattgtttttcccgacaaattatcaaacgacccatcattgcactctttcaaaatttcattctcagacgtaccattcttttttttttttctccgggaagatgagatatgctcattcttgaaagtgcctccgggcttgccttctgcacacttctttccctccctgtctacgccatggtagcgtccgcctaggttgcaggcgacccggggggtggggcacaccattcaaagaaggggagggattgaggtttgcatcaaaacaaatacccctgcctttgcaaaggccataactaagtaatccagaaaaagaaatgcaggcggagaatagcagcctccctctgccaagtaagaggaaccggcctaaaggacattttctctctctctcctcccctctcatcgggtgaatagtgagctgctccg

PROBLEM #3

CODE:


p53='cggagcagctcactattcacccgatgagaggggaggagagagagagaaaatgtcctttag\
gccggttcctcttacttggcagagggaggctgctattctccgcctgcatttctttttctg\
gattacttagttatggcctttgcaaaggcaggggtatttgttttgatgcaaacctcaatc\
cctccccttctttgaatggtgtgccccaccccccgggtcgcctgcaacctaggcggacgc\
taccatggcgtagacagggagggaaagaagtgtgcagaaggcaagcccggaggcactttc\
aagaatgagcatatctcatcttcccggagaaaaaaaaaaaagaatggtacgtctgagaat\
gaaattttgaaagagtgcaatgatgggtcgtttgataatttgtcgggaaaaacaatctac\
ctgttatctagctttgggctaggccattccagttccagacgcaggctgaacgtcgtgaag\
cggaaggggcgggcccgcaggcgtccgtgtggtcctccgtgcagccctcggcccgagccg\
gttcttcctggtaggaggcggaactcgaattcatttctcccgctgccccatctcttagct\
cgcggttgtttcattccgcagtttcttcccatgcacctgccgcgtaccggccactttgtg\
ccgtacttacgtcatctttttcctaaatcgaggtggcatttacacacagcgccagtgcac\
acagcaagtgcacaggaagatgagttttggcccctaaccgctccgtgatgcctaccaagt\
cacagacccttttcatcgtcccagaaacgtttcatcacgtctcttcccagtcgattcccg\
accccacctttattttgatctccataaccattttgcctgttggagaacttcatatagaat\
ggaatcaggatgggcgctgtggctcacgcctgcactttggctcacgcctgcactttggga\
ggccgaggcgggcggattacttgaggataggagttccagaccagcgtggccaacgtggtg'

standard = { 'ttt': 'F', 'tct': 'S', 'tat': 'Y', 'tgt': 'C',
		'ttc': 'F', 'tcc': 'S', 'tac': 'Y', 'tgc': 'C',
		'tta': 'L', 'tca': 'S', 'taa': '*' , 'tca': '*',
		'ttg': 'L', 'tcg': 'S', 'tag': '*', 'tcg': 'W',

		'ctt': 'L', 'cct': 'P', 'cat': 'H', 'cgt': 'R',
		'ctc': 'L', 'ccc': 'P', 'cac': 'H', 'cgc': 'R',
		'cta': 'L', 'cca': 'P', 'caa': 'Q', 'cga': 'R',
		'ctg': 'L', 'ccg': 'P', 'cag': 'Q', 'cgg': 'R',

 		'att': 'I', 'act': 'T', 'aat': 'N', 'agt': 'S',
 		'atc': 'I', 'acc': 'T', 'aac': 'N', 'agc': 'S',
		'ata': 'I', 'aca': 'T', 'aaa': 'K', 'aga': 'R',
  		'atg': 'M', 'acg': 'T', 'aag': 'K', 'agg': 'R',

		'gtt': 'V', 'gct': 'A', 'gat': 'D', 'ggt': 'G',
		'gtc': 'V', 'gcc': 'A', 'gac': 'D', 'ggc': 'G',
		'gta': 'V', 'gca': 'A', 'gaa': 'E', 'gga': 'G',
		'gtg': 'V', 'gcg': 'A', 'gag': 'E', 'ggg': 'G'
		}

print 'Amino Acid Sequence of Translated DNA'

Protein=''
for n in [0,1,2]:
    for p in range(n,len(p53),n+3):
        if p53[p:p+3] in standard:
            Protein += standard[p53[p:p+3]]
    print n+1
    print Protein
    Protein=''

print 'Amino Acid Sequence of Translated Reverse Complemented DNA'

p53=p53.replace('a','T')
p53=p53.replace('t','a')
p53=p53.replace('c','G')
p53=p53.replace('g','c')
p53=p53.lower()
p53=p53[::-1]

Protein=''
for n in [0,1,2]:
    for p in range(n,len(p53),n+3):
        if p53[p:p+3] in standard:
            Protein += standard[p53[p:p+3]]
    print n+1
    print Protein
    Protein=''

OUTPUT
<code><pre>

Amino Acid Sequence of Translated DNA
1
RSS*LFTREGRRERENVL*AGSSYLAEGGCYSPPAFLFLDYLVMAFAKAGVFVLMQT*IPPLLMVCPTPRVACNLGGRYHGVDREGKKCAEGKPGGTFKNEHI*SSRRKKKKNGTSENEILKECNDGWFDNLWGKTIYLLSSFGLGHSSSRRRLNVVKRKGRARRRPCGPPCSPRPEPVLPGRRRNWN*FLPLPHLLARGCFIPQFLPMHLPRTGHFVPYLRHLFPKWRHLHTAPVHTASAQEDEFPLTAPCLPSHRPF*WSQKRFITSLPSRFPTPPLFSP*PFCLLENFI*NGIRMGAVAHACTLAHACTLGGRGGRITG*EFQTSVANVV
2
GQ*YHREGREEEMP*PFSTGEELYLAAFFLILVLARRVLFMKLILPLEGCPPRWLN*RRTVTGGRVAKQPEHFRHSISGKKKEGRNKFKSQDGVDIVGKNYCISLAGIQSDQLTRKGGRPQRRPRQPGRPFSGGANRFFSAPILAALFFAFFHHCATALVRLRIFPNEITTRSHQKARREFALPSATSTTFHVQNFIRSPVIPPTLFIPNICCGN*INEQMACATLT*AAFGARGGYDGFRQVPRV
3
EALHDEEERKS*RPYGRGLLPIFLL*MLQAGLLAPISFGATPWCPARPADGEKCKKRAFESIIPRKKNYLNNEQMWIWKQYVLFAASFDREWKEGAQVCSRSWPPSLRATNISLPSARVIAFPACRRTVVYHFLWVIHSQHSVQRSPPPMYSQP*VRRHRLQDPPLFIHPLCELYNNGGCLAHHLLGPARYE*VRSGTV
Amino Acid Sequence of Translated Reverse Complemented DNA
1
HHVGHAGLELLS*SNPPAWASQSAGVSQSAGVSHSAHPDSILYEVLQQAKLR*K*RGREWTGKRRDETFLGRKGSVT*A*RSG*GPKLIFLCTCCVHRCV*MPPRFRKKMT*VRHKVAGTRQVHGKKLRNETTAS*EMGQREKIRVPPPTRKNRLGPRAARRTTRTPAGPPLPLHDVQPASGTGMA*PKAR*QVDCFSRQIIKRPIIALFQNFILRRTILFFFSPGRDMLILESASGLAFCTLLSLPVYAMVASA*VAGDPGGGAHH*KKGRDGLHQNKYPCLCKGHN*VIQKKKCRRRIAASLCQVRGTGLKDIFSLSPPL*WGE*AAP
2
TRGTLNPSQ*PPLAPKAAEQVRVAQAISFIEFPQQMLGIKKVGGITGERMNFTKVVLVAHEGRAK*LLALCCLRVVMHWFGKMRSRTSAVAQCKNANKNAARMGAENNRFAPPENGRPGCRGHRRCGRPPFRVSCSEMPAKLIQ*LFPTI*TP*CLFKFFQRPSFFFPEMDCHLKCSGCFATLPPVTHVRR*LRDRGGHP*RGRIRLIKKTLLARHTSIRKKAAR*SSSPVENG*GISSSLP*R*ECP
3
PLHLIQNAPAPVGEKARASPLSSMVPRKVG*IGGGRGEVEVRKGVLR*EVGK*FVLCAGCVCPIGKDKRQGARHENRQALRGARWFPYGNAGRCGTTRAPPP*TQCLTNPPSDQRVSTLKT*ALKFSDTSFFSEY*LKPGCSTSPPLPVVPVRTGHHKRRLVHKNPPAG*KIERCAEALSQKEGKTFSLPLREVLP

PROBLEM #4

CODE:


import random

standard = { 'ttt': 'F', 'tct': 'S', 'tat': 'Y', 'tgt': 'C',
		'ttc': 'F', 'tcc': 'S', 'tac': 'Y', 'tgc': 'C',
		'tta': 'L', 'tca': 'S', 'taa': '*' , 'tga': '*',
		'ttg': 'L', 'tcg': 'S', 'tag': '*', 'tgg': 'W',

		'ctt': 'L', 'cct': 'P', 'cat': 'H', 'cgt': 'R',
		'ctc': 'L', 'ccc': 'P', 'cac': 'H', 'cgc': 'R',
		'cta': 'L', 'cca': 'P', 'caa': 'Q', 'cga': 'R',
		'ctg': 'L', 'ccg': 'P', 'cag': 'Q', 'cgg': 'R',

 		'att': 'I', 'act': 'T', 'aat': 'N', 'agt': 'S',
 		'atc': 'I', 'acc': 'T', 'aac': 'N', 'agc': 'S',
		'ata': 'I', 'aca': 'T', 'aaa': 'K', 'aga': 'R',
  		'atg': 'M', 'acg': 'T', 'aag': 'K', 'agg': 'R',

		'gtt': 'V', 'gct': 'A', 'gat': 'D', 'ggt': 'G',
		'gtc': 'V', 'gcc': 'A', 'gac': 'D', 'ggc': 'G',
		'gta': 'V', 'gca': 'A', 'gaa': 'E', 'gga': 'G',
		'gtg': 'V', 'gcg': 'A', 'gag': 'E', 'ggg': 'G'
		}

def translate_and_count_stops(z):

    Protein=''
    for n in range(0,len(z),3):
        if z[n:n+3] in standard:
            Protein += standard[z[n:n+3]]

    print 'Amino Acid Sequence of Translated DNA'
    print Protein
    print 'Total number of stop codons'
    print Protein.count('*')

gene = raw_input('Enter your sequence:\n')

m = input('How many mutations?')
                 
mutationspots=random.sample(range(0,len(gene),1),m)
#print mutationspots

gene_list = list(gene)

for y in mutationspots:
    newnucleotide = random.choice('ATCG')
    while newnucleotide == gene_list[y]:
        newnucleotide = random.choice('ATCG')
    gene_list[y] = newnucleotide

gene_new = ''.join(gene_list)

print '\nMutated Sequence\n'
print gene_new

print 'Original Gene\n'
translate_and_count_stops(gene)

print '\nOriginal Genes with Random Mutations\n'
gene_new=gene_new.lower()
translate_and_count_stops(gene_new)

OUTPUT:


Enter your sequence:
cggagcagctcactattcacccgatgagaggggaggagagagagagaaaatgtcctttag
gccggttcctcttacttggcagagggaggctgctattctccgcctgcatttctttttctg
gattacttagttatggcctttgcaaaggcaggggtatttgttttgatgcaaacctcaatc
cctccccttctttgaatggtgtgccccaccccccgggtcgcctgcaacctaggcggacgc
taccatggcgtagacagggagggaaagaagtgtgcagaaggcaagcccggaggcactttc
aagaatgagcatatctcatcttcccggagaaaaaaaaaaaagaatggtacgtctgagaat
gaaattttgaaagagtgcaatgatgggtcgtttgataatttgtcgggaaaaacaatctac
ctgttatctagctttgggctaggccattccagttccagacgcaggctgaacgtcgtgaag
cggaaggggcgggcccgcaggcgtccgtgtggtcctccgtgcagccctcggcccgagccg
gttcttcctggtaggaggcggaactcgaattcatttctcccgctgccccatctcttagct
cgcggttgtttcattccgcagtttcttcccatgcacctgccgcgtaccggccactttgtg
ccgtacttacgtcatctttttcctaaatcgaggtggcatttacacacagcgccagtgcac
acagcaagtgcacaggaagatgagttttggcccctaaccgctccgtgatgcctaccaagt
cacagacccttttcatcgtcccagaaacgtttcatcacgtctcttcccagtcgattcccg
accccacctttattttgatctccataaccattttgcctgttggagaacttcatatagaat
ggaatcaggatgggcgctgtggctcacgcctgcactttggctcacgcctgcactttggga
ggccgaggcgggcggattacttgaggataggagttccagaccagcgtggccaacgtggtg

How many mutations?10

Mutated Sequence

cggagcagctcactattcacccgatgagaggggaggagagagagagaaaatgtcctttag
gGcggttcctcttacttggcagagggaggctgctattctccgcctgcatttctttttctg
gattacttagttatggcctttgcaaaggcaggggtatttgttttgatgcaaacctcaatc
cctccccttctttgaatggtgtgccccaccccccgggtcgcctgcaacctaggcggacgc
taccatggcgtagacagggagggaaagaagtgtgcagaaggcaaCcccggaggcactttc
aagaGtgagcatatctcatcttcccggagaaaaaaaaaaaagaatggtacgtctgagaat
gaaattttgaaagagtgcaatgatgggtcgtttgataatttgtcgggaaaaacaatctac
ctgttatctagctttgggctaggccattccagttccagacgcaggctgaAcgtcgtgaag
cggaaggggcgggcccgcaggcgtccgtgtggtcctccgtgcCgccctcggcccgagccg
gttcttcctggtaggaGgcggaactcgaattcatttctcccgctgccccatctcGtagct
cgcggttgtttcattccgcagtttcttcccatgcacctgccgcgtaCcggccactttgtg
ccgtacttacgtcatctttttcctaaatcgaggtggcatttacacacagcgccagtgcac
acagcaagtgcacaggaagatgagttttggcccctaaccgctccgtgatgcctaccCaGt
cacagacccttttcatcgtcccagaaacgtttcatcacgtctcttcccagtcgattcccg
accccacctttattttgatctccataaccattttgcctgttggagaacttcatatagaat
ggaatcaggatgggcgctgtggctcacgcctgcactttggctcacgcctgcactttggga
ggccgaggcgggcggattacttgaggataggagttccagaccagcgtggccaacgtggtg

Original Gene

Amino Acid Sequence of Translated DNA
RSSSLFTR*EGRRERENVL*RFLLLGRGRLLFSACISFSIT*LWPLQRQGYLF*CKPQPPLL*MVCPTPRVACNLGGRPWRRQGGKEVCRRQARRHFRMSISHLPGEKKKRMVRLREILKECNDGSFDNLSGKTIYVI*LWARPFQFQTQAERREGRGGPAGVRVVLRAALGPSVLPGRRRNSNSFLPLPHLLARLFHSAVSSHAPAAYRPLCRTYVIFFLNRGGIYTQRQCTASAQEDEFWPLTAP*CLPSQTLFIVPETFHHVSSQSIPPHLYFDLHNHFACWRTSYRGIRMGAVAHACTLAHACTLGPRRADYLRIGVPDQRGQRG
Total number of stop codons
7

Original Genes with Random Mutations

Amino Acid Sequence of Translated DNA
RSSSLFTR*EGRRERENVL*RFLLLGRGRLLFSACISFSIT*LWPLQRQGYLF*CKPQPPLL*MVCPTPRVACNLGGRPWRRQGGKEVCRRQPRRHFRVSISHLPGEKKKRMVRLREILKECNDGSFDNLSGKTIYVI*LWARPFQFQTQAERREGRGGPAGVRVVLRAALGPSVLPGRRRNSNSFLPLPHLVARLFHSAVSSHAPAAYRPLCRTYVIFFLNRGGIYTQRQCTASAQEDEFWPLTAP*CLPSQTLFIVPETFHHVSSQSIPPHLYFDLHNHFACWRTSYRGIRMGAVAHACTLAHACTLGPRRADYLRIGVPDQRGQRG
Total number of stop codons
7

MORE OUTPUTS (ONLY STOP CODONS COUNT REPORTED):


>>> 
Total number of stop codons
7
Total number of stop codons
7
>>> ================================ RESTART ================================
>>> 
Total number of stop codons
7
Total number of stop codons
7
>>> ================================ RESTART ================================
>>> 
Total number of stop codons
7
Total number of stop codons
7
>>> ================================ RESTART ================================
>>> 
Total number of stop codons
7
Total number of stop codons
7
>>> ================================ RESTART ================================
>>> 
Total number of stop codons
7
Total number of stop codons
7
>>> ================================ RESTART ================================
>>> 
Total number of stop codons
7
Total number of stop codons
6
>>> ================================ RESTART ================================
>>> 
Total number of stop codons
7
Total number of stop codons
8
>>> ================================ RESTART ================================
>>> 
Total number of stop codons
7
Total number of stop codons
7
>>>
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