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

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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


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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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