Rosalind第70题：Global Alignment with Scoring Matrix

Problem

To penalize symbol substitutions differently depending on which two symbols are involved in the substitution, we obtain a scoring matrix  in which  represents the (negative) score assigned to a substitution of the th symbol of our alphabet  with the th symbol of .

A gap penalty is the component deducted from alignment score due to the presence of a gap. A gap penalty may be a function of the length of the gap; for example, a linear gap penalty is a constant  such that each inserted or deleted symbol is charged ; as a result, the cost of a gap of length  is equal to .

Given: Two protein strings  and  in FASTA format (each of length at most 1000 aa).

Return: The maximum alignment score between  and . Use:

• The BLOSUM62 scoring matrix.
• Linear gap penalty equal to 5 (i.e., a cost of -5 is assessed for each gap symbol).

• 为了根据替换涉及哪两个符号来不同地惩罚符号替换，我们获得一个得分矩阵  在其中  表示分配给替代项的（负）得分 我们字母的th符号  与 的符号 。

  甲缺口罚分是从比对得分扣除组分由于一个存在间隙。空位罚分可以是空位长度的函数。例如， 线性间隙罚分是一个常数 这样每个插入或删除的符号都会收费 ; 结果，长度差距的代价 等于 。

  给出：两个蛋白质串  和 以FASTA格式（每个长度最大为1000 aa）。

  返回值：之间的最大对齐分数 和 。采用：

• 该BLOSUM62得分矩阵。
• 线性间隙罚分等于5（即，每个间隙符号的评估成本为-5 ）。

Sample Dataset

>Rosalind_67
PLEASANTLY
>Rosalind_17
MEANLY

Sample Output

8