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Lesson VI - The Community Science Project

Author(s): Anne Rosenwald1, Gaurav Arora2, Vinayak Mathur3

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

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Summary:
Genome Solver's Community Science Project was developed as a way to use the skills taught in the previous lessons. We're asking members of the community to provide instances of potential phage genes embedded in bacterial genomes.

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

Version 1.0 - published on 31 Oct 2018 doi:10.25334/Q4XT68 - cite this Last public release: 2.0

Keywords

  1. Bioinformatics Education
  2. Bioinformatics and Genomics

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Description

Genome Solver's Community Science Project was developed as a way to use the skills taught in the preceding Lessons for an exploration into mechanisms for generating bacterial diversity. We're asking members of the community to provide instances of potential horizontal gene transfer between bacteriophages and bacteria by looking for phage genes embedded in bacterial genomes. With these data, we aim to examine the roles that horizontal gene transfer play in diversity and evolution of bacteria.

First, there is a slide deck and transcript to introduce the project and some of the work the Genome Solver developers have published on this topic.  

To join the project and help us explore this form of horizontal gene transfer, please look at the Word document in this Lesson called "CSP_Workflow."  If you need help getting started (such as finding a gene to begin with or a species of bacteria to investigate), let us know at genomesolver12@gmail.com.  Note there are also two Excel spreadsheets in this Lesson.  One is for collecting your "forward" BLAST hits - when you take a phage gene and find bacterial homologs.  The second is for collecting your "reverse" BLAST hits - when you take your top bacterial hit and look for additional viral (phage) homologs.  These two spreadsheets will then be uploaded to a Google Form, which you can access here: https://goo.gl/forms/EclEkDnBAH4MBLom1

 

 

Notes

Materials were updated as of Fall 2018.  Note that because the slide decks and exercises point to external websites and web-based tools, some of the illustrations contained in the materials may not look exactly like the live website.  Functionality is usually unchanged. 

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