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Research Article

An Integrative Method for Accurate Comparative Genome Mapping

  • Firas Swidan mail,

    To whom correspondence should be addressed. E-mail: Swidanf@janelia.hhmi.org

    Affiliations: Department of Computer Science, Technion, Israel Institute of Technology, Haifa, Israel, Janelia Farm Research Center, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America

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  • Eduardo P. C Rocha,

    Affiliations: Atelier de Bioinformatique, University Paris VI, Paris, France, Unité GGB, Institut Pasteur, Paris, France

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  • Michael Shmoish,

    Affiliation: Department of Computer Science, Technion, Israel Institute of Technology, Haifa, Israel

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  • Ron Y Pinter

    Affiliation: Department of Computer Science, Technion, Israel Institute of Technology, Haifa, Israel

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  • Published: August 04, 2006
  • DOI: 10.1371/journal.pcbi.0020075

Reader Comments (1)

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It's a shame that the abstract doesn't contain details of the results.

Posted by danbolser on 30 Nov 2008 at 11:04 GMT

The abstract is somewhat like an invitation to read the paper, rather than a summary of the paper's results. While the general findings are described at a high level (and seem very impressive), their is no way to judge the results as no data are presented. For example, one section reads:

"We demonstrate both MAGIC's robustness and scalability: the former is asserted with respect to its initial input and with respect to its parameters' values. The latter is asserted by applying MAGIC to distantly related organisms and to large genomes."

Other than the fact that MAGIC's robustness and scalability have been 'asserted', what can I judge from this general statement?It would be great to have a quantification of these observations. The abstract continues:

"We compare MAGIC to other comparative mapping methods and provide detailed analysis of the differences between them. Our improvements allow a comprehensive study of the diversity of genetic repertoires resulting from large-scale mutations."

Although this all sounds great, it actually tells me nothing about how good the method is other than the vague suggestion of improvements (i.e. are these general improvements? improvements across the board? improvements across what board? improvements in one are? improvements in which area? significant improvements?)


To summarise my overall comment with one specific example, it would be really great to see a summary of the: "... comprehensive study of the diversity of genetic repertoires resulting from large-scale mutations."

Can a 'detail centric' abstract appear as a reply to this comment? I think this would greatly increase the quality and accessibility of the work, which is already clearly at high level.