This project was prepared as part of a BioQUEST faculty development workshop entitled BioQUEST 2004 Summer Workshop for Undergraduate Faculty: Systems Biology at Beloit College in June 2004. The BioQUEST Curriculum Consortium is committed to the reform of undergraduate biology instruction through an emphasis on engaging students in realistic scientific practices. This approach is sometimes characterized as an inquiry driven approach and is captured in BioQUEST's three P's (problem-posing, problem-solving, and peer-persuasion). As part of this workshop groups of faculty were encouraged to initiate innovative curricular projects. We are sharing these works in progress in the hope that they will stimulate further exploration, collaboration and development. Please see the following links for additional information:

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Rice Phylogeny Revisited
 
 
Authors          Audiences          Overview           Materials          Resources           Future Directions
 

 


Authors


Noppadon Khiripet
National Electronics and Computer Technology Center


Devi Prasad Potluri
Chicago State University

 
   
 


Possible Audiences:

Graduate students,Researchers, Taxonomists,Computer Science students  

 
 


Brief Overview:

Reevaluate and visualize relationships using phylogenetic trees, Benzer plots, and circular plots.  

 
   
 


Project Materials:

Noppadon: I wrote two PERL scripts to help reformat the files that JBenzer and GDE needed. The first one is "clustdist2benzer.pl" which takes the clustalw distant matrix (by the "clustaldist" option of Biology Workbench) and according to a given threshold, it produces an associated matrix that can be used with JBenzer. The second script is "benzer2gde.pl", which takes the jbenzer input file and transforms into a file that can be used with the GDE. Devi Prasad: I chose the enzymes used in the study, obtained the sequences from NCBI, constructed phylogenetic trees using Clustalw [Biology Workbench], converted the data back to distance mastrix ClustalDist[Biology Workbench]  

 
 


Resources and References:

Biology Workbench -- http://workbench.sdsc.edu
GoVisual Diagram Editor -- http://www.oreas.com
JBenzer -- http://www.beloit.edu/~biology/benzer.html
NCBI genebank  

 
   
 


Future Directions:

1.Students are free to explore and modify the codes.
2.What is the right threshold for clustering using jBenzer and GDE, why ?
3.Reconstruct the phylogenetic tree from the combined matrix using tree drawing tools.  

 
 


Attachments


- clustdist2benzer.pl
- benzer2gde.pl
- RICE_PHYLOGENY.ppt