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#165, v2.0 Published:
#600, v1.0.0 Published:

Title

Old VersionNew Version
1Using DNA Subway to Analyze Sequence Relationships 1Intro to DNA Barcoding

Authors

Old VersionNew Version
1Elizabeth F Ryder (Worcester Polytechnic Institute) 1Elizabeth Ryder (Worcester Polytechnic Institute)
2Jason Williams (DNA Learning Center) 2Elizabeth Doyle (James Madison University)
3William Tapprich (University of Nebraska-Omaha) 3William Tapprich (University of Nebraska-Omaha) 
4Emily Lescak (University of Alaska) 4Emily Lescak ()
5Oliver Hyman (The Department of Biology, James Madison University; The Center for Genome & Metagenome Studies, James Madison University ) 5Oliver Hyman (The Department of Biology, James Madison University; The Center for Genome & Metagenome Studies, James Madison University ) 
6Ray A. Enke (The Department of Biology, James Madison University; The Center for Genome & Metagenome Studies, James Madison University ) 6Ray A Enke (The Department of Biology, James Madison University; The Center for Genome & Metagenome Studies, James Madison University )
7Sam S Donovan (University of Pittsburgh) 7Sam S Donovan (University of Pittsburgh) 
8Hayley Orndorf (University of Pittsburgh) 8Hayley Orndorf (University of Pittsburgh) 
  9Hayley Orndorf () 
  10Andrea Pesce (James Madison University) 

Description

Old VersionNew Version
1<p>These are instructions for a 120-minute bioinformatics lab in which students will learn how to use the DNA Subway (<a href="http://www.dnasubway.org">http://www.dnasubway.org</a>) Blue Line. DNA Subway is an online educational bioinformatics platform. It bundles research-grade bioinformatics tools, high-performance computing, and databases into workflows with an easy-to-use interface. The Blue Line is a workflow for analyzing DNA bar-coding data to determine the taxonomic identity of an organism and examine inferred phylogenetic relationships among species. The data analyzed in this exercise is a collection of mosquito DNA sequences generated by students at James Madison University. Identification of a mosquito&rsquo;s genus is important because different mosquitoes are capable of carrying different pathogens causing deadly human diseases.</p>  1<p>Materials include:</p>
2  2  
3<p>Note: A natural way to divide this material may be to cover everything up to section IV (Phylogenetic Trees) in one class, leaving additional time to address trees in as much depth as desired.</p> 3<ol>
   4   <li>&nbsp;A&nbsp;short pre-class assignment</li>
   5   <li>A slide deck introducing DNA Barcoding, DNA Subway Blue Line and a short Blue Line activity</li>
   6   <li>Two &quot;unknown&quot; Sanger sequencing reads for the Blue Line activity</li>
   7</ol>

Attachments

1 file — ./Jason Williams - barcoding_intro.pptx 1 file — ./Enke Adaptation/Bugs to Barcode Lecture-Enke.pptx
2 file — ./Using-DNA-Subway-to-Analyze-Sequence-Barcodes-05182018-Instructor.docx 2 file — ./Enke Adaptation/DNA Subway Blue Line pre class assignment-Enke.docx
3 file — ./Using-DNA-Subway-to-Analyze-Sequence-Barcodes-05182018-Student.docx 3 file — ./Enke Adaptation/unknown_plant_F_read.ab1
4 file — ./dna_subway_image.png 4 file — ./Enke Adaptation/unknown_plant_R_read.ab1
5 file — publication_647_678/dna_subway_image.png
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