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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 
method.

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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