Corpus ID: 8555604

Practical aspects of Compressed Suffix Arrays and FM-Index in Searching DNA Sequences

@inproceedings{Hon2004PracticalAO,
  title={Practical aspects of Compressed Suffix Arrays and FM-Index in Searching DNA Sequences},
  author={W. Hon and T. Lam and W. Sung and Wai-Leuk Tse and C. Wong and S. Yiu},
  booktitle={ALENEX/ANALC},
  year={2004}
}
Searching patterns in the DNA sequence is an important step in biological research. To speed up the search process, one can index the DNA sequence. However, classical indexing data structures like suffix trees and suffix arrays are not feasible for indexing DNA sequences due to main memory requirement, as DNA sequences can be very long. In this paper, we evaluate the performance of two compressed data structures, Compressed Suffix Array (CSA) and FM-index, in the context of searching and… Expand
34 Citations
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