Abstract
Identification of regions with untypical percentage G+C composition anddinucleotide signatures are two genome analysis techniques used in theidentification of horizontallyacquired DNA. We describe a generic programframework for performing both types of analysis in linear time. Theapproach is extended for length >2 oligonucleotide signatures. Using the derived program we test some of the conclusions of Karlin and Burge, the primary exponents of these techniques. We demonstrate that no singlemethod of signature analysis is sufficient for the complete identificationof horizontally acquired DNA. Consequently we produce a fast program -and a robust methodology - for the production and employment genomesignatures in the identification of horizontally acquired DNA.