Rosalind第100题：Overlap Alignment

Problem

An overlap alignment between two strings  and  is a local alignment of a suffix of  with a prefix of . An optimal overlap alignment will therefore maximize an alignment score over all such substrings of  and .

The term "overlap alignment" has also been used to describe what Rosalind defines as a semiglobal alignment. See “Semiglobal Alignment” for details.

Given: Two DNA strings  and  in FASTA format, each having length at most 10 kbp.

Return: The score of an optimal overlap alignment of  and , followed by an alignment of a suffix  of  and a prefix  of  achieving this optimal score. Use an alignment score in which matching symbols count +1, substitutions count -2, and there is a linear gap penalty of 2. If multiple optimal alignments exist, then you may return any one.

两个字符串之间的重叠对齐 和 是后缀的局部对齐有前缀的。因此，最佳的重叠对齐方式将使所有这样的子字符串的对齐方式得分最大化 和 。

术语“重叠对齐”也已用于描述Rosalind定义为半 全局对齐的内容。有关详细信息，请参见“半全局对齐”。

给出：两个DNA字符串  和 以FASTA格式，每个长度最大为10 kbp。

返回值：的最佳重叠比对得分 和 ，然后对齐后缀  的  和一个前缀  的 达到最佳分数。使用对齐分数，其中匹配符号的计数为+1，替代符号的计数为-2，线性间隙罚分为2。如果存在多个最佳对齐，则可以返回任何一个。

Sample Dataset

>Rosalind_54
CTAAGGGATTCCGGTAATTAGACAG
>Rosalind_45
ATAGACCATATGTCAGTGACTGTGTAA

Sample Output

1
ATTAGAC-AG
AT-AGACCAT