Computer Science

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Author: search.filters.author.Salzberg, Steven L.Subject: search.filters.subject.genomes

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    A clustering method for repeat analysis in DNA sequences.
    (Genome Biology, 2001-08-01) Volfovsky, Natalia; Haas, Brian J.; Salzberg, Steven L.
    Background: A computational system for analysis of the repetitive structure of genomic sequences is described. The method uses suffix trees to organize and search the input sequences; this data structure has been used previously for efficient computation of exact and degenerate repeats. Results: The resulting software tool collects all repeat classes and outputs summary statistics as well as a file containing multiple sequences (multi fasta), that can be used as the target of searches. Its use is demonstrated here on several complete microbial genomes, the entire Arabidopsis thaliana genome, and a large collection of rice bacterial artificial chromosome end sequences. Conclusions: We propose a new clustering method for analysis of the repeat data captured in suffix trees. This method has been incorporated into a system that can find repeats in individual genome sequences or sets of sequences, and that can organize those repeats into classes. It quickly and accurately creates repeat databases from small and large genomes. The associated software (RepeatFinder), should prove helpful in the analysis of repeat structure for both complete and partial genome sequences.
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    Versatile and open software for comparing large genomes
    (Genome Biology, 2004-01-30) Kurtz, Stefan; Phillippy, Adam; Delcher, Arthur L.; Smoot, Michael; Shumway, Martin; Antonescu, Corina; Salzberg, Steven L.
    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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    The Genome Assembly Archive: A New Public Resource
    (PLoS Biology, 2004-09) Salzberg, Steven L.; Church, Deanna; DiCuccio, Michael; Yaschenko, Eugene; Ostell, James