Time Limit: 1000MS | Memory Limit: 10000K | |
Total Submissions: 13576 | Accepted: 7511 |
Description
A human gene can be identified through a series of time-consuming biological experiments, often with the help of computer programs. Once a sequence of a gene is obtained, the next job is to determine its function.
One of the methods for biologists to use in determining the function of a new gene sequence that they have just identified is to search a database with the new gene as a query. The database to be searched stores many gene sequences and their functions – many researchers have been submitting their genes and functions to the database and the database is freely accessible through the Internet.
A database search will return a list of gene sequences from the database that are similar to the query gene.
Biologists assume that sequence similarity often implies functional similarity. So, the function of the new gene might be one of the functions that the genes from the list have. To exactly determine which one is the right one another series of biological experiments will be needed.
Your job is to make a program that compares two genes and determines their similarity as explained below. Your program may be used as a part of the database search if you can provide an efficient one.
Given two genes AGTGATG and GTTAG, how similar are they? One of the methods to measure the similarity
of two genes is called alignment. In an alignment, spaces are inserted, if necessary, in appropriate positions of
the genes to make them equally long and score the resulting genes according to a scoring matrix.
For example, one space is inserted into AGTGATG to result in AGTGAT-G, and three spaces are inserted into GTTAG to result in –GT--TAG. A space is denoted by a minus sign (-). The two genes are now of equal
length. These two strings are aligned:
AGTGAT-G
-GT--TAG
In this alignment, there are four matches, namely, G in the second position, T in the third, T in the sixth, and G in the eighth. Each pair of aligned characters is assigned a score according to the following scoring matrix.
![](https://i-blog.csdnimg.cn/blog_migrate/fcf3938cf314f4598e568b157e91a600.gif)
denotes that a space-space match is not allowed. The score of the alignment above is (-3)+5+5+(-2)+(-3)+5+(-3)+5=9.
Of course, many other alignments are possible. One is shown below (a different number of spaces are inserted into different positions):
AGTGATG
-GTTA-G
This alignment gives a score of (-3)+5+5+(-2)+5+(-1) +5=14. So, this one is better than the previous one. As a matter of fact, this one is optimal since no other alignment can have a higher score. So, it is said that the
similarity of the two genes is 14.
Input
Output
Sample Input
2 7 AGTGATG 5 GTTAG 7 AGCTATT 9 AGCTTTAAA
Sample Output
14 21
Source
这道题目很不错。
题目大意是:给定两组DNA序列,要你求出它们的最大相似度
每个字母与其他字母或自身和空格对应都有一个打分,求在这两个字符串中插入空格,让这两个字符串的匹配分数最大
解题思路,模仿动态规划里面经典的求最长公共子序列的方法
dp[i][j]表示字符串s1 1-i的和字符串序列s2 1-j的最长公共子序列的长度
当s1[i] == s2[j] 时dp[i][j] = dp[i-1][j-1] + 1
当s1[i] != s2[j]时,dp[i][j] = max(dp[i-1][j], dp[i][j-1]);
然后这个思想运用到这个题目中
dp[i][j]用来表示字符串s1 1-i的和字符串序列s2 1-j的最大相似度
value(s1[i], s2[j])表示字符s1[i]和s2[j]的匹配值
dp[i][j] 为 dp[i-1][j-1] + value(s1[i], s2[j]), dp[i-1][j] + value(s1[i], '-'), dp[i][j-1] + value('-', s2[j])中的最大值
这里要处理一下边界值
dp[0][0] = 0;
dp[0][j] = dp[0][j-1] + value('-', s2[j])
dp[i][0] = dp[i-1][0] + value(s1[i], '-');
dp[0][i]表示字符串s1前i个字符串和长度为i的空格串匹配的值
最后结果就为dp[len1][len2]
#include <iostream>
#include <cstdio>
#include <cmath>
#include <cstring>
#include <map>
using namespace std;
const int maxn = 110;
int t, len1, len2, dp[maxn][maxn], index1[maxn][5], index2[maxn][5];
int matrix[5][5] = {{5,-1,-2,-1,-3},
{-1,5,-3,-2,-4},
{-2,-3,5,-2,-2},
{-1,-2,-2,5,-1},
{-3,-4,-2,-1,0}};
char s1[maxn], s2[maxn];
map<char, int> dictionary;
void LCS();
int main()
{
dictionary['A'] = 0, dictionary['C'] = 1, dictionary['G'] = 2, dictionary['T'] = 3, dictionary['-'] = 4;
scanf("%d", &t);
while(t-- != 0)
{
scanf("%d %s", &len1, s1+1);
scanf("%d %s", &len2, s2+1);
LCS();
printf("%d\n", dp[len1][len2]);
}
return 0;
}
void LCS()
{
dp[0][0] = 0;
for(int i = 1; i <= len1; i++)
{
dp[i][0] = matrix[dictionary[s1[i]]][dictionary['-']] + dp[i-1][0];
}
for(int j = 1; j <= len2; j++)
{
dp[0][j] = matrix[dictionary['-']][dictionary[s2[j]]] + dp[0][j-1];
}
for(int i = 1; i <= len1; i++)
{
for(int j = 1; j <= len2; j++)
{
dp[i][j] = dp[i-1][j-1] + matrix[dictionary[s1[i]]][dictionary[s2[j]]];
dp[i][j] = max(dp[i][j], dp[i-1][j] + matrix[dictionary[s1[i]]][dictionary['-']]);
dp[i][j] = max(dp[i][j], dp[i][j-1] + matrix[dictionary['-']][dictionary[s2[j]]]);
}
}
}