提取其他两个保守字符串之间的字符串，并考虑python或R中的不匹配

Question

如果这里有副本，我深表歉意。就我所寻找的而言，我还没有找到这个问题的答案

我有上千个DNA序列，大约50个碱基（50个字符）长。 我在中间有一个可变的序列，范围从6~30 bp。 两个保守序列；一个在变量序列的左侧和右侧，长度约为10 bp！ 我的数据是这样的

ATTGCGCGA NAAANNNANNNNNNA CGAAAATTTA

ATTGCGCGA = conserved area on the left (reference)

NAAANNNANNNNNNA = random sequence between 

CGAAAATTTA = conserved area on the right (reference)

到目前为止还不错。我知道如何提取保守区域之间的字符串； 然而，有时我预计保守区域会出现错误。 我想找到一种方法，允许保守区域出现一些不匹配（例如，两个或三个不匹配），并提取它们之间的任何序列/字符串，长度介于 6-30bp

我的数据是这样的

1 ATTGCGCGA NAAANNNANNNNNNA CGAAAATTTA # it looks good
2 ATTGCGCGA NAAANNNAN  CGAAAATTTA      # it looks good
3 ATTGCGCGA NAA CGAAAATTTA             # the variable sequence is too short
4 ATASGCGCGA NAAGGNNN CGAfATTTA        # two mismatches on the left and two on the right conserved sequences
5 ATASjkCGCGA NAAGGNNN CGAfjfkdfTTA    # more than 3 mismatches at the left area and more than 3 mismatches at the right area
6 ATTGCGCGA NAAGGNNN CGAfjfkdfTTA      # more than 3 mismatches at the left conserved area

我希望我的输出像这样

1 NAAANNNANNNNNNA # it looks good
2 NAAANNNAN       # it looks good
4 NAAGGNNN        # two mismatches on the left and two on the right conserved sequences

！！！重要的 我的数据没有被分割成有间隙的块。我把它放在这里是为了让它直观易懂 原始数据如下所示

1 ATTGCGCGANAAANNNANNNNNNACGAAAATTTA # it looks good
2 ATTGCGCGANAAANNNANCGAAAATTTA       # it looks good
3 ATTGCGCGANAACGAAAATTTA             # the variable sequence is too short
4 ATASGCGCGANAAGGNNNCGAfATTTA        # two mismatches on the left and two on the right conserved sequences
5 ATASjkCGCGANAAGGNNNCGAfjfkdfTTA    # more than 3 mismatches at the left area and more than 3 mismatches at the right area
6 ATTGCGCGANAAGGNNNCGAfjfkdfTTA      # more than 3 mismatches at the left conserved area

Answer 1

每行有3个部分。让我们称之为X Y Z.
你对Y感兴趣，但你说有时X&；Z有一些变化

您应该使用Levenshtein distance来检查实际X&；Z向官方X&；Z

如果“距离”足够小，你可以选择Y

请参见here了解python库，该库将计算距离