SLiMFinder: A Probabilistic Method for Identifying Over-Represented, Convergently Evolved, Short Linear Motifs in Proteins

Richard J. Edwards; Norman E. Davey; Denis C. Shields

doi:10.1371/journal.pone.0000967

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Peer-reviewed

Research Article

SLiMFinder: A Probabilistic Method for Identifying Over-Represented, Convergently Evolved, Short Linear Motifs in Proteins

Richard J. Edwards ,

*To whom correspondence should be addressed. E-mail: r.edwards@soton.ac.uk

Affiliations University College Dublin Complex and Adaptive Systems Laboratory, University College Dublin Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin, Ireland, School of Biological Sciences, University of Southampton, Southampton, United Kingdom
⨯
Norman E. Davey,

Affiliation University College Dublin Complex and Adaptive Systems Laboratory, University College Dublin Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin, Ireland
⨯
Denis C. Shields

Affiliation University College Dublin Complex and Adaptive Systems Laboratory, University College Dublin Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin, Ireland
⨯

SLiMFinder: A Probabilistic Method for Identifying Over-Represented, Convergently Evolved, Short Linear Motifs in Proteins

Richard J. Edwards,
Norman E. Davey,
Denis C. Shields

Published: October 3, 2007
https://doi.org/10.1371/journal.pone.0000967

About the Authors

Richard J. Edwards

*To whom correspondence should be addressed. E-mail: r.edwards@soton.ac.uk

Affiliations University College Dublin Complex and Adaptive Systems Laboratory, University College Dublin Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin, Ireland, School of Biological Sciences, University of Southampton, Southampton, United Kingdom

Norman E. Davey

Affiliation University College Dublin Complex and Adaptive Systems Laboratory, University College Dublin Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin, Ireland

Denis C. Shields

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: RE. Performed the experiments: RE. Analyzed the data: RE. Wrote the paper: DS RE. Other: Assisted in algorithm development: ND.

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Sequence motif analysis
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BLAST algorithm
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Protein sequencing
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Phage display
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Endoplasmic reticulum
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Human genomics
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Molecular evolution
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Algorithms
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