UNIT 10.3 Using MUMmer to Identify Similar Regions in Large Sequence Sets

  1. Arthur L. Delcher1,
  2. Steven L. Salzberg2,
  3. Adam M. Phillippy2

Published Online: 1 FEB 2003

DOI: 10.1002/0471250953.bi1003s00

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Delcher, A. L., Salzberg, S. L. and Phillippy, A. M. 2003. Using MUMmer to Identify Similar Regions in Large Sequence Sets. Current Protocols in Bioinformatics. 00:10.3:10.3.1–10.3.18.

Author Information

  1. 1

    The Institute for Genomic Research Rockville, Maryland and Computer Science Department, Loyola College in Maryland, Baltimore, Maryland

  2. 2

    The Institute for Genomic Research, Rockville, Maryland

Publication History

  1. Published Online: 1 FEB 2003
  2. Published Print: JAN 2003


The MUMmer sequence alignment package is a suite of computer programs designed to detect regions of homology in long biological sequences. Version 2.1 makes several improvements to the package, including: increased speed and reduced memory requirements; the ability to handle both protein and DNA sequences; the ability to handle multiple sequence fragments; and new algorithms for clustering together basic matches. The system is particularly efficient at comparing highly similar sequences, such as alternative versions of fragment assemblies or closely related strains of the same bacterium.