since you have M small strings using KMP or RabinKarp will take time O(mn) but with suffix tree you can do it in O(n+m) read these and you'll be able to construct one: http://www.cs.helsinki.fi/u/ukkonen/SuffixT1withFigs.pdf http://www.cise.ufl.edu/~sahni/dsaaj/enrich/c16/suffix.htm
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