Can I use BLAST to compare 2 non-biological strings?

I know what BLAST (The Basic Local Alignment Search Tool) was designed for. But I am interested in using such advanced te开发者_JS百科xt comparison and its final effects.

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You could use vmatch.

If you want to use a tool for local alignment of subtrings, you might want to use STELLAR though, paper: http://www.biomedcentral.com/1471-2105/12/S9/S15/

It does everything blast does, but has quite convenient option to use chars.