Accurateidentificationofprotein-codingregions(exons)inDNAsequenceshasbeenachallengingtaskinbioinformatics.Particularlythecodingregionshavea3-baseperiodicity,whichformsthebasisofallexonidentificationmethods.Manysignalprocessingtoolsandtechniqueshavebeenappliedsuccessfullyfortheidentificationtaskbutstillimprovementinthisdirectionisneeded.Inthispaper,wehaveintroducedanewpromisingmodel-independenttime-frequencyfilteringtechniquebasedonS-transformforaccurateidentificationofthecodingregions.TheS-transformisapowerfullineartime-frequencyrepresentationusefulforfilteringintime-frequencydomain.Thepotentialoftheproposedtechniquehasbeenassessedthroughsimulationstudyandtheresultsobtainedhavebeencomparedwiththeexistingmethodsusingstandarddatasets.Thecomparativestudydemonstratesthattheproposedmethodoutperformsitscounterpartsinidentifyingthecodingregions.