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PatMaN: rapid alignment of short sequences to large databases

By Kay Prüfer, Udo Stenzel, Michael Dannemann, Richard E. Green, Michael Lachmann and Janet Kelso


Summary: We present a tool suited for searching for many short nucleotide sequences in large databases, allowing for a predefined number of gaps and mismatches. The commandline-driven program implements a non-deterministic automata matching algorithm on a keyword tree of the search strings. Both queries with and without ambiguity codes can be searched. Search time is short for perfect matches, and retrieval time rises exponentially with the number of edits allowed

Topics: Applications Note
Publisher: Oxford University Press
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Provided by: PubMed Central

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