Aligning ESTs to Genome Using Low Frequency High Density Index

Abstract

The development of computer and information technology facilitates many researches of biology that employ computer software. In this paper, we provide a method that can align the ESTs to the genome. Yet, the human genome contains repetitive sequences that hold one-tenth of the human genome. And in the past, most of the associated researches cannot handle those repetitive sequences well, and even cannot deal with those sequences. Hence, our research hopes to handle both those repetitive and unique sequences in the genome to make all ESTs can be aligned to the correct regions. In this way, we can employ the results to have an advance research and analysis. We provide different strategies that can save time and get results within an acceptable correctness to align a single EST and the entire ESTs in dbEST to the genome. We consider the low frequency and high density index problem to provide the EST to locate to the genome. And then, we propose a heuristic algorithm and employ MUGUP to check our research with different test sets of ESTs.