Abstract
The work to determine the sequences of the three billion chemical base pairs (bps) which compose human DNA has been done by Human Genome Project (HGP). One of the most significant challenges in bioinformatics is to discover all of the estimated 30,000 to 35,000 human genes and highlight important functional elements from the gene sequence among these three billion bps. In this paper, we studied 117 orthologous human and mouse gene pairs according to the theory of Comparative Genomic Approach, and concluded three kinds of alignment types on orthologous gene around the start and stop codons. An efficient external sorting algorithm and some gene length restrictions have been introduced into our two-pass sorting algorithms to generate possible orthologous gene pair candidates from human and mouse DNA sequences. Our algorithm was further verified by the experiments which adopt 31 orthologous human and mouse gene pairs as the training data. The experimental results proved the capability of our approach to discover most of the 31 orthologous gene pairs once the parameters were properly set. The tools BLAST and LAP2 were additionally employed to analyze our results, and to pick out more probable orthologous gene candidates.