Indexing similar DNA sequences

LNCS v. 6124 is Proceedings of the 6th International Conference, AAIM 2010To study the genetic variations of a species, one basic operation is to search for occurrences of patterns in a large number of very similar genomic sequences. To build an indexing data structure on the concatenation of all sequences may require a lot of memory. In this paper, we propose a new scheme to index highly similar sequences by taking advantage of the similarity among the sequences. To store r sequences with k common segments, our index requires only O(n + N logN) bits of memory, where n is the total length of the common segments and N is the total length of the distinct regions in all texts. The total length of all sequences is rn + N, and any scheme to store these sequences requires Ω(n + N) bits. Searching for a pattern P of length m takes O(m+mlogN +mlog(rk)psc(P)+occ log n), where psc(P) is the number of prefixes of P that appear as a suffix of some common segments and occ is the number of occurrences of P in all sequences. In practice, rk ≤ N, and psc(P) is usually a small constant. We have implemented our solution1 and evaluated our solution using real DNA sequences. The experiments show that the memory requirement of our solution is much less than that required by BWT built on the concatenation of all sequences. When compared to the other existing solution (RLCSA), we use less memory with faster searching time. © Springer-Verlag Berlin Heidelberg 2010.link_to_subscribed_fulltextThe 6th International Conference on Algorithmic Aspects in Information and Management (AAIM 2010), Shandong, China, 19-21 July 2010. In Lecture Notes in Computer Science, v. 6124, p. 180-19