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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

Abstract

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
OAI identifier: oai:pubmedcentral.nih.gov:2718670
Provided by: PubMed Central

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Citations

  1. (1988). A finite state machine algorithm for finding restriction sites and other pattern matching applications.
  2. (1990). Basic local alignment search tool.
  3. (1975). Efficient string matching: an aid to bibliographic search.
  4. (2002). Flexible Pattern Matching in Strings: Practical On-line Search Algorithms for Texts and Biological Sequences.
  5. (1986). Improved programs for DNAand protein sequence analysis on the IBM personal computer and other standard computer systems.

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