> 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?