[Biojava-l] Behavior of the createRegex() method (MotifTool class)

[Sylvain Foisy]

Hi,


I used the createRegex() method to return a regular expression from a
sequence of DNA inputted by the user to scan a genome for that motif. I just
discovered an interesting thing about that method: if n is in the motif to
seek, the regex will not have n as a possibility.

Ok, I have that motif: atgnnnndgta.

CreateRegex would return: atg[atcg]{4}gta and it does

What if my sequence to scan contains n: atgagcngta, for exemple.
Java.util.regex would not find the pattern. Unless mistaken, the pattern
should be atg[atcgn]{4}gta.

Am I wrong? Any input would be appreciated

Sylvain

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Sylvain Foisy, Ph. D
Directeur des operations
BioneQ - Reseau quebecois de bioinformatique
Universite de Montreal/Genome-Quebec
1260 rue Crescent, Bur. 201
Montreal, QC
H3G 2A9
Tel.: (514) 878-9911
Fax : (514) 878-2899
E-Mail:sylvain.foisy@bioneq.qc.ca
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