Question

I am trying to find pattern search with specific condition: we have to find starting positions. Also more than one mismatch is allowed ie. it should be run for 1 or 2 or 3 mismatch. i.e. for 1 mismatch one character of the pattern may or may not match while matching with the sequence. As same for 2 mismatch two character of the pattern may or may not match while matching with the sequence. And so on.

output: should be written into a file in a table format:
e.g,  pattern may be TGCA and sequence may be ATCGATGCATATCGATC....]

finding TGCA  in sequence ATCGATGATATCGATC  will result in
S.no  position       the_matched_pattern
1      5                 TGCA

配对和错配可能处于任何地位(即处于相同地位或处于不同地位)。我如何执行?

Answer 1

总的来说,这是最常见的次消费问题。是否对“Smith-Waterman”算法进行了一些研究——你或许应该这样做。

http://en.wikipedia.org/wiki/Smith-Waterman_algorithm

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