CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing

Pradipta Ray; Suyash Shringarpure; Mladen Kolar; Eric P. Xing

doi:10.1371/journal.pcbi.1000090

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Open Access

Peer-reviewed

Research Article

CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing

Pradipta Ray ,

Contributed equally to this work with: Pradipta Ray, Suyash Shringarpure

Affiliation School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
⨯
Suyash Shringarpure ,

Contributed equally to this work with: Pradipta Ray, Suyash Shringarpure

Affiliation School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
⨯
Mladen Kolar,

Affiliation School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
⨯
Eric P. Xing

* E-mail: eric.xing@gmail.com

Affiliation School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
⨯

CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing

Pradipta Ray,
Suyash Shringarpure,
Mladen Kolar,
Eric P. Xing

Published: June 6, 2008
https://doi.org/10.1371/journal.pcbi.1000090

About the Authors

Pradipta Ray

Contributed equally to this work with: Pradipta Ray, Suyash Shringarpure

Affiliation School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America

Suyash Shringarpure

Contributed equally to this work with: Pradipta Ray, Suyash Shringarpure

Affiliation School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America

Mladen Kolar

Affiliation School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America

Eric P. Xing

* E-mail: eric.xing@gmail.com

Affiliation School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: EX. Performed the experiments: PR SS. Analyzed the data: PR SS MK EX. Wrote the paper: EX. Designed the model: EX.

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Sequence motif analysis
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Phylogenetic analysis
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Sequence alignment
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Phylogenetics
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Multiple alignment calculation
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Algorithms
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Drosophila melanogaster
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Nucleotides
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