我要做一个函数,打印一段DNA中最长的回文子串。我已经写了一个函数来检查一段DNA本身是否是一个词缀。请看下面的函数。
def make_complement_strand(DNA):
complement=[]
rules_for_complement={"A":"T","T":"A","C":"G","G":"C"}
for letter in DNA:
complement.append(rules_for_complement[letter])
return(complement)
def is_this_a_palindrome(DNA):
DNA=list(DNA)
if DNA!=(make_complement_strand(DNA)[::-1]):
print("false")
return False
else:
print("true")
return True
is_this_a_palindrome("GGGCCC")
但是现在:如何制作一个打印DNA字符串最长的palindrome子串的函数?
在遗传学的背景下,palindrome的含义与用于单词和句子的定义略有不同。由于双螺旋是由两条成对的核苷酸链形成的,这两条核苷酸链在5'-到3'的意义上运行方向相反,而且核苷酸总是以相同的方式配对(DNA的腺嘌呤(A)与胸腺嘧啶(T),RNA的乌拉基尔(U);胞嘧啶(C)与鸟嘌呤(G)),因此,如果一个(单链)核苷酸序列与它的反向补码相等,就说它是一个顺位。例如,DNA序列ACCTAGGT是palindromic,因为它的核苷酸比补码是TGGATCCA,把补码中的核苷酸顺序颠倒过来,就会得到原始序列。
在这里,这应该是获取最长手印子串的一个不错的起点。
def make_complement_strand(DNA):
complement=[]
rules_for_complement={"A":"T","T":"A","C":"G","G":"C"}
for letter in DNA:
complement.append(rules_for_complement[letter])
return(complement)
def is_this_a_palindrome(DNA):
DNA=list(DNA)
if DNA!=(make_complement_strand(DNA)[::-1]):
#print("false")
return False
else:
#print("true")
return True
def longest_palindrome_ss(org_dna, palindrone_func):
'''
Naive implementation-
We start with 2 pointers.
i starts at start of current subsqeunce and j starts from i+1 to end
increment i with every loop
Uses palindrome function provided by user
Further improvements-
1. Start with longest sequence instead of starting with smallest. i.e. start with i=0 and j=final_i and decrement.
'''
longest_palin=""
i=j=0
last_i=len(org_dna)
while i < last_i:
j=i+1
while j < last_i:
current_subsequence = org_dna[i:j+1]
if palindrone_func(current_subsequence):
if len(current_subsequence)>len(longest_palin):
longest_palin=current_subsequence
j+=1
i+=1
print(org_dna, longest_palin)
return longest_palin
longest_palindrome_ss("GGGCCC", is_this_a_palindrome)
longest_palindrome_ss("GAGCTT", is_this_a_palindrome)
longest_palindrome_ss("GGAATTCGA", is_this_a_palindrome)
下面是一些执行结果 -
mahorir@mahorir-Vostro-3446:~/Desktop$ python3 dna_paln.py
GGGCCC GGGCCC
GAGCTT AGCT
GGAATTCGA GAATTC