Is there Java implementation of regular expression search of sequence

David Guzman david_aaron at softhome.net
Mon Jun 2 04:00:46 EST 2003


There are interesting projects such as Biojava (http://biojava.org/) maybe
it can be useful, but I think there is no need to replace the native
EMBOSS implementation. Currently, at biojava, EMBOSS support is under
development, but under bioperl works fine (that's the one I use). The best
choice would be the design of an interface written in java (based in
biojava...), it should work, ...certainly, it works for Jemboss (graphical
interface of EMBOSS in java). Or take the source code of the EMBOSS
programs of interest and port them tp java (EMBOSS is open source). Well
my advice would be... contact biojava team... Good Luck.

david_aaron at softhome.net

> I am a software developer in a microbiology lab. EMBOSS has functions
> such as DREG, PREG to do the regular expression search of a nucleotide
> sequence. Since most of our own softwares are programmed in JAVA, I am
> trying to find the JAVA implementation of DREG, PREG, and FUZZNUC and
> FUZZPRO so that we can import these ambiguity sequence searching
> functions into our own softwares.
> Thanks for any help!
> Adele
> Biochemistry and Microbiology
> University of Victoria
> BC, Canada
> adelej at uvic.ca
> ---

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