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ALL HITS ALL THE TIME: PARAMETER FREE CALCULATION OF SEED SENSITIVITY
2007
Proceedings of the 5th Asia-Pacific Bioinformatics Conference
Standard search techniques for DNA repeats start by identifying seeds, that is, small matching words, that may inhabit larger repeats. Recent innovations in seed structure have led to the development of spaced seeds [8] and indel seeds [9] which are more sensitive than contiguous seeds (also known as k-mers, k-tuples, l-words, etc.). Evaluating seed sensitivity requires 1) specifying a homology model which describes types of alignments that can occur between two copies of a repeat, and 2)
doi:10.1142/9781860947995_0035
fatcat:2nqoll4o7jaorafrmmk6qb5dei