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ASM-Clust: classifying functionally diverse protein families using alignment score matrices

Speth, Daan R. and Orphan, Victoria J. (2019) ASM-Clust: classifying functionally diverse protein families using alignment score matrices. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20191004-102107177

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Abstract

Rapid advances in sequencing technology have resulted in the availability of genomes from organisms across the tree of life. Accurately interpreting the function of proteins in these genomes is a major challenge, as annotation transfer based on homology frequently results in misannotation and error propagation. This challenge is especially pressing for organisms whose genomes are directly obtained from environmental samples, as interpretation of their physiology and ecology is often based solely on the genome sequence. For complex protein (super)families containing a large number of sequences, classification can be used to determine whether annotation transfer is appropriate, or whether experimental evidence for function is lacking. Here we present a novel computational approach for de novo classification of large protein (super)families, based on clustering an alignment score matrix obtained by aligning all sequences in the family to a small subset of the data. We evaluate our approach on the enolase family in the Structure Function Linkage Database.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/792739DOIDiscussion Paper
ORCID:
AuthorORCID
Speth, Daan R.0000-0002-2361-5935
Orphan, Victoria J.0000-0002-5374-6178
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. bioRxiv preprint first posted online Oct. 3, 2019. This work was supported by the US Department of Energy, Office of Science, Office of Biological and Environmental Research under award number DE-SC0016469 to Victoria J. Orphan. Daan R. Speth was supported by the Netherlands Organisation for Scientific Research, Rubicon award 019.153LW.039.
Funders:
Funding AgencyGrant Number
Department of Energy (DOE)DE-SC0016469
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)019.153LW.039
Record Number:CaltechAUTHORS:20191004-102107177
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20191004-102107177
Official Citation:ASM-Clust: classifying functionally diverse protein families using alignment score matrices. Daan R Speth, Victoria J Orphan. bioRxiv 792739; doi: https://doi.org/10.1101/792739
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:99083
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:04 Oct 2019 17:31
Last Modified:04 Oct 2019 17:31

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