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Genome Solver - A bioinformatics pipeline for community science

Author(s): Vinayak Mathur1, Gaurav Arora2, Anne Rosenwald3

1. Cabrini University 2. Gallaudet University 3. Georgetown University

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The Genome Solver was an NSF-funded project developed as a way to train undergraduate life science faculty in basic web-based tools for bioinformatics. As part of the project we developed a one-day workshop consisting of bioinformatics modules on…

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The Genome Solver was an NSF-funded project developed as a way to train undergraduate life science faculty in basic web-based tools for bioinformatics. As part of the project we developed a one-day workshop consisting of bioinformatics modules on the theme of bacterial genomics, which we delivered to faculty at colleges and universities around the country. All of our workshop material can be accessed on the QUBESHub website: https://qubeshub.org/community/groups/genomesolver/

Licensed under CC Attribution-ShareAlike 4.0 International according to these terms

Version 1.0 - published on 20 Feb 2024 doi:10.25334/SEDX-YS29 - cite this

Keywords

  1. phylogenetics
  2. bacteriophage
  3. bacteria
  4. Horizontal Gene transfer
  5. Genome Analysis

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Description

The Genome Solver was an NSF-funded project developed as a way to train undergraduate life science faculty in basic web-based tools for bioinformatics. As part of the project we developed a one-day workshop consisting of  bioinformatics modules on the theme of bacterial genomics,  which we delivered to faculty at colleges and universities around the country. All of our workshop material can be accessed on the QUBESHub website: https://qubeshub.org/community/groups/genomesolver/

One of our main initiatives is a Community Science Project that explores horizontal gene transfer (HGT) between bacteria and the phages that infect them by investigating the vast wealth of phage and bacterial sequences currently in public databases.  We invite faculty and their students to participate in the search for examples of this type of HGT. All that is needed is a computer, an internet connection, and enthusiasm for research. Our own work has demonstrated that undergraduates can produce publishable data using this approach.   By pooling all the information from a variety of small projects under the umbrella of the Genome Solver Community Science Project, we will be able to make broad and fundamental hypotheses about the role that HGT from bacteriophages plays in bacterial evolution. 

Next-Gen Genome Solver was supported by a grant from the National Science Foundation (DUE 1505102). 

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