Publication - Journal Article Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding

https://doi.org/10.1093/bioadv/vbad005
Description

Christine H Chang, William C Nelson, Abby Jerger, Aaron T Wright, Robert G Egbert, Jason E McDermott, Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding, Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad005, https://doi.org/10.1093/bioadv/vbad005.

 

Funding Acknowledgments

This work was supported by the Department of Energy (DOE) Office of Biological and Environmental Research (BER) and is a contribution of the Scientific Focus Area ‘Persistence Control of Engineered Functions in Complex Soil Microbiomes’, the DOE/BER ‘Improved Protein Annotation in KBase Using Machine Learning, Multi-Omics Data Integration, and Structural Prediction’ project, the DOE/BER ‘Machine-Learning Approaches for Integrating Multi-Omics Data to Expand Microbiome Annotation’ project, NSF [1856556], the Defense Threat Reduction Agency, under Interagency Agreement [DTRA13081–37739], and the Proxy Applications for Converged Workloads (PACER) project, a component of the Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory. PNNL is operated for the DOE by Battelle Memorial Institute under Contract [DE-AC05-76RL01830].

Software Data Analysis
Functional Annotation Analysis
Python
Snakemake
DNA Sequence Analysis
RNA Sequence Analysis
Kmers
Projects (1)
Project
Persistence Control of Engineered Functions in Complex Soil Microbiomes (PerCon SFA), Secure Biosystems Design Project

Last updated on 2023-02-23T19:37:46+00:00 by LN Anderson PerCon SFA Project Publication Experimental Data Catalog The Persistence Control of Engineered Functions in Complex Soil Microbiomes Project (PerCon SFA) at Pacific Northwest National Laboratory ( PNNL ) is a Genomic Sciences Program...

Scientific Discovery
Biology
Microbiome Science
Earth System Science

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English
People (4)
Jason McDermott

Dr. Jason McDermott, senior research scientist, has extensive research experience in molecular and structural virology and data resource design, data integration and prediction of biological networks, bridging experimental and computational biology. Currently, his research interests include data...

Aaron Wright

Aaron Wright leads the Chemical Biology & Exposure Sciences Group in the Biological Sciences Division at PNNL. His highly collaborative and diverse chemical biology research team is focused on gaining an improved functional and mechanistic understanding of biological processes including: (a)...

Dr William C Nelson

Dr. Nelson’s background is in genomic analysis of microbial organisms. He spent 10 years at The Institute for Genomic Research (TIGR), first as a data analyst and then as the team lead for Microbial Annotation. He was involved in some of the earliest bacterial genome sequencing projects, including...

Robert Egbert

Biography I am a biological engineer working to advance high-throughput biological engineering for rapid optimization of complex gene clusters and dynamical systems in microbes through pooled genomic library assembly, high-throughput sequencing and variant scoring. I utilize machine learning...

Software (1)
Snekmer: A scalable pipeline for protein sequence fingerprinting using amino acid recoding (AAR)