Re: [Seqan-dev] I have a question !! :)

["Weese, David" <weese@campus.fu-berlin.de>]

Hi,

I'm not the author of this Finder, but the source code seems to allow only repeats of character classes. You need repeated sequences.

Please have a look at the original publication of the wildcard shift-and algorithm in:

Navarro, Raffinot, "Flexible Pattern Matching in Strings" (2002), section 4.3.1

Regards,

David

--
David Weese weese@inf.fu-berlin.de
Freie Universität Berlin http://www.inf.fu-berlin.de/
Institut für Informatik Phone: +49 30 838 75246
Takustraße 9 Algorithmic Bioinformatics
14195 Berlin Room 021 

Am 11.11.2010 um 10:53 schrieb 김미정:

 

Hi, I’m Mi jeong Kim and student from korea.

I attend to class about Topics in Bioinformatics.

We studied about convenience of alignment tool by using SeqAn at last week

and found the use of wildcard braces { }.

But we couldn’t use braces.

 

The core of this mail !!

 

We want to know the using of the braces at this situation.

for example

GCGTTGCGCGCGCTTTATCGTTGCGCTTATGC

(GC) <- repeat

 

We tried many pattern

For example

1.     needle = “(GC){2, 4}”

2.     needle = “GC{2, 4}”

3.     needle = “GC{2, 4}+”

4.     needle = “GC+{2, 4}”

5.     needle = “(GC)+{2, 4}”

………

but this program didn’t work.

 

Could you tell me how to use the braces at this situation ?

 

 

Thank you for read my awkward mail and hope you to answer me.

Have a nice day !

 

 

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