Constructing benchmark test sets for biological sequence analysis using independent set algorithms

Samantha Petti; Sean R. Eddy

doi:10.1371/journal.pcbi.1009492

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Open Access

Peer-reviewed

Research Article

Constructing benchmark test sets for biological sequence analysis using independent set algorithms

Samantha Petti,

Roles Conceptualization, Data curation, Formal analysis, Funding acquisition, Methodology, Software, Visualization, Writing – original draft, Writing – review & editing

Affiliation NSF-Simons Center for the Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, Massachusetts, United States of America

https://orcid.org/0000-0001-8281-8161

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Sean R. Eddy

Roles Conceptualization, Funding acquisition, Resources, Supervision, Writing – review & editing

* E-mail: seaneddy@fas.harvard.edu

Affiliation Howard Hughes Medical Institute; Department of Molecular & Cellular Biology; and John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America

https://orcid.org/0000-0001-6676-4706

⨯

Constructing benchmark test sets for biological sequence analysis using independent set algorithms

Samantha Petti,
Sean R. Eddy

Published: March 7, 2022
https://doi.org/10.1371/journal.pcbi.1009492
See the preprint

About the Authors

Samantha Petti

Roles Conceptualization, Data curation, Formal analysis, Funding acquisition, Methodology, Software, Visualization, Writing – original draft, Writing – review & editing

Affiliation NSF-Simons Center for the Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, Massachusetts, United States of America

https://orcid.org/0000-0001-8281-8161

Sean R. Eddy

Roles Conceptualization, Funding acquisition, Resources, Supervision, Writing – review & editing

* E-mail: seaneddy@fas.harvard.edu

Affiliation Howard Hughes Medical Institute; Department of Molecular & Cellular Biology; and John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America

https://orcid.org/0000-0001-6676-4706

Competing Interests

The authors have declared that no competing interests exist.

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Cobalt
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Machine learning algorithms
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Sequence alignment
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Algorithms
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BLAST algorithm
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Multiple alignment calculation
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Machine learning
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Protein domains
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