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      Versatile and open software for comparing large genomes

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes.

          Abstract

          The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes. Two new graphical viewing tools provide alternative ways to analyze genome alignments. The new system is the first version of MUMmer to be released as open-source software. This allows other developers to contribute to the code base and freely redistribute the code. The MUMmer sources are available at http://www.tigr.org/software/mummer.

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          Most cited references23

          • Record: found
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          Identification of common molecular subsequences.

          T.F. Smith, M.S. Waterman (1981)
          Article 0 comments Cited 1696 times – based on 0 reviews     Review now
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            Basic Local Alignment Search Tool

            S Altschul (1990)
            Article 0 comments Cited 1455 times – based on 0 reviews     Review now
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              Improved tools for biological sequence comparison.

              W R Pearson, D J Lipman (1988)
              We have developed three computer programs for comparisons of protein and DNA sequences. They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity. The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched. FASTA includes an additional step in the calculation of the initial pairwise similarity score that allows multiple regions of similarity to be joined to increase the score of related sequences. The RDF2 program can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition. The LFASTA program can display all the regions of local similarity between two sequences with scores greater than a threshold, using the same scoring parameters and a similar alignment algorithm; these local similarities can be displayed as a "graphic matrix" plot or as individual alignments. In addition, these programs have been generalized to allow comparison of DNA or protein sequences based on a variety of alternative scoring matrices.
              Article 0 comments Cited 845 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Biol
                Title: Genome Biology
                Publisher: BioMed Central (London )
                ISSN (Print): 1465-6906
                ISSN (Electronic): 1465-6914
                Publication date (Print): 2004
                Publication date (Electronic): 30 January 2004
                Volume: 5
                Issue: 2
                Page: R12
                Affiliations
                [1 ]Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
                [2 ]The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
                [3 ]Current address: Department of Computer Science, University of Virginia, Charlottesville, VA 22904, USA
                Article
                Publisher ID: gb-2004-5-2-r12
                DOI: 10.1186/gb-2004-5-2-r12
                PMC ID: 395750
                PubMed ID: 14759262
                SO-VID: b402db10-0397-42fe-b4de-a57b387a056d
                Copyright © Copyright © 2004 Kurtz et al.; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.
                History
                Date received : 27 October 2003
                Date revision received : 15 December 2003
                Date accepted : 17 December 2003
                Categories
                Subject: Software

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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