This project was prepared as part of a BioQUEST faculty development workshop entitled Bioinformatics in Biology Education: Working with Sequence, Structure and Function at Oklahoma City Community College in January 2005. 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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Bioinformatics Introductory Module: Use of Bioinformatics Tools in Genome Assembly and Annotation
 
 
Authors          Audiences          Overview           Materials          Resources           Future Directions
 

 


Authors


Edgar Scott II
University of Oklahoma Health Sciences Center


Terry Schwaner
North Georgia College & State University


Michael Turnage
Southeastern Oklahoma State University

 
   
 


Possible Audiences:

Mathematics, Computer Science, Biology Faculty 3rd and 4th Year College/University Students Advanced (AP) Hight School Students  

 
 


Brief Overview:

What is Bioinformatics and what are some of the tools? This lab is divided into a 1hr lecture and a 1hr lab assignment. A description of the lab was created specifically for this module that defines bioinformatics and introduces concepts such as pairwise sequence alignments, database searching, and open reading frame prediction. The assignment at the end of the lab document places the student in a genome sequencing lab as a bioinformatician whose responsibility is to assembly reads, identify reading frames in the assembled contig, and blasting the potential genes against a protein database such as UniProt or ExPASy.  

 
   
 


Project Materials:

Bioinformatics websites:
UniProt - website for protein sequence information
ExPASy - website for protein sequence information
ScreenVec - website for identifying possible vector contaminations
CAP3 Sequence Assembly Program - website for assembling read sequences
ORF finder - website for identifying potential reading frames
 

 
 


Resources and References:

Bioinformatics Introductory Module - Website with the lab assignment, example sequences, and links to bioinformatics tools online.

Books - list of bioinformatics books  

 
   
 


Future Directions:

Would like to create more modules that biology and computer science professors could implement into their classes to expose undergraduate students to bioinformatics.