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Re^3: string match using with an N in any position

by BrowserUk (Pope)
on Nov 18, 2011 at 23:48 UTC ( #938927=note: print w/ replies, xml ) Need Help??


in reply to Re^2: string match using with an N in any position
in thread string match using with an N in any position

The code of Re: string match using with an N in any position matches 'CACGT' against 'CBCGTNNN' ('B' vice 'N').

Agreed. But in the genomic encoding scheme of things, the 'N' means 'aNy'. Whereas 'B' means 'any except A'.

With my very limited understanding, 'N' therefore encompasses 'B' in as much as there is no mention in his post of excluding strings that have an 'A' in the wild-card position. Nor is there any mention in the post of the possibility of "targets"(*) ever contains 'B's in the relevant positions.

In this case, the OP seems satisfied with the solution for his particular problem. I'll leave it up to him to know his data and problem domain.

(*An unusual term in this context -- the wild-cards are usually in the query -- but whatever :)


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Comment on Re^3: string match using with an N in any position
Re^4: string match using with an N in any position
by AnomalousMonk (Abbot) on Nov 19, 2011 at 16:17 UTC
    ... in ... genomic encoding ... 'N' means 'aNy' [w]hereas 'B' means 'any except A'.

    I did not know that.

    With my very limited understanding...

    Well, your understanding is nowhere near as limited as mine and, as you say, the OPer seems happy, so...

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