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I am a software developer in a microbiology lab. EMBOSS ...

Peter Rice pmr at ebi.ac.uk
Wed May 7 04:15:12 EST 2003

adele wrote:
> 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.

dreg and preg are simple regular expression matches ... so any regular 
expression library would do.

fuzznuc, fuzzpro and fuzztran use a wide range of matching algorithm, 
depending on the pattern ... although you could use just the brute force 

One solution is to write the code yourself.

Another is to use a web services implementation and invoke that from 
Java. There are various web services implementations of EMBOSS. At EBI 
we use SoapLab. Maybe CBR in Halifax can help you?

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