With the increasingly popularity of genome sequencing, transforming such raw sequence data into knowledge remains a hard task. This project will develop an application for gene prediction using development tools such as Perl and PHP. The project will identify stretches of sequence for genomic DNA that is biologically functional including protein coding regions. The 3 steps that involve are transcription, splicing and translation. Transcription is the process of copying DNA to RNA. Meanwhile, splicing is a modification of genetic information after a few transcriptions. The process determines introns (useless information) and exons (useful information) in DNA sequence. Hidden Markov Model which is a mathematical functional will be used in this step to predict the DNA sequence. The introns will be removed while the exons will be combined together to produce the mRNA. The final step is the translation which is the process by which mRNA is translated into proteins. The protein sequence is the final output of Gene Prediction System. More knowledge on gene prediction will be explored in order to get better understanding of how gene prediction works.