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Research Article

DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies

  • Shaun Mahony mail,

    To whom correspondence should be addressed. E-mail: shaun.mahony@ccbb.pitt.edu (SM); benos@pitt.edu (PVB)

    Affiliations: Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, Department of Computer Science, Faculty of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America

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  • Philip E Auron,

    Affiliations: Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America, Department of Molecular Genetics and Biochemistry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America

    X
  • Panayiotis V Benos mail

    To whom correspondence should be addressed. E-mail: shaun.mahony@ccbb.pitt.edu (SM); benos@pitt.edu (PVB)

    Affiliations: Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America

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  • Published: March 30, 2007
  • DOI: 10.1371/journal.pcbi.0030061

About the Authors

Shaun Mahony, Panayiotis V Benos
Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
Shaun Mahony
Department of Computer Science, Faculty of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
Philip E Auron
Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
Philip E Auron
Department of Molecular Genetics and Biochemistry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
Panayiotis V Benos
Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
Panayiotis V Benos
University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America

Corresponding Authors

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

SM and PVB conceived and designed the experiments. SM performed the experiments and contributed reagents/materials/analysis tools. SM, PEA, and PVB analyzed the data and wrote the paper.