Inexact Local Alignment Search over Suffix Arrays

Department of Computer Science, University of Maryland, College Park, MD 20742, USA.
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine 11/2009; 2009(1-4):83-97. DOI: 10.1109/BIBM.2009.25
Source: PubMed


We describe an algorithm for finding approximate seeds for DNA homology searches. In contrast to previous algorithms that use exact or spaced seeds, our approximate seeds may contain insertions and deletions. We present a generalized heuristic for finding such seeds efficiently and prove that the heuristic does not affect sensitivity. We show how to adapt this algorithm to work over the memory efficient suffix array with provably minimal overhead in running time.We demonstrate the effectiveness of our algorithm on two tasks: whole genome alignment of bacteria and alignment of the DNA sequences of 177 genes that are orthologous in human and mouse. We show our algorithm achieves better sensitivity and uses less memory than other commonly used local alignment tools.

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    • "Note that if we fail to align the first say α characters of sequence i (ith sequence in the sorted list), and the common prefix of sequence i and sequence i + 1 is longer than α, we do not need to try to align sequence i + 1 at all. The search algorithm is very similar to the algorithm in [17], except that the backtracking threshold is fixed as the given radius of the clusters. We use the ternary quick sort algorithm [18] once, in the beginning, to sort the sequences lexicographically. "
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