Trees, Arrays, Networks and Optimization for Finding Patterns in Biological Sequences

author: Dan Gusfield, University of California
published: Feb. 25, 2007,   recorded: November 2005,   views: 5415


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a) The use of suffix trees and integer programming for finding optimal virus signatures. b) A current treatment of suffix-arrays and their uses. In the last several years simple linear-time algorithms for building suffix arrays have been developed making explicit suffix-trees mostly obsolete. c) Algorithms for finding signatures (patterns) of historical recombination and gene-conversion in SNP (binary) sequences. The techniques here relate to graph-theory.

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