A survey on disk-based genome sequence indexing

Abstract

Due to recent remarkable advances in genome sequencing technologies, the DNA sequences of many living organisms including the human being have been collected in databases. To fully harness the genome databases, we should need the technologies for efficient indexing and searching the genome sequences, and the suffix tree has been adopted in many recent research papers. In this paper, we survey the most up-to-date indexing algorithms that construct the disk-based suffix trees for genome sequences and compare their strengths/weaknesses and performance.