BLAST that Gene

Overview & Concepts

Students will use the NCBI BLAST site and OMIM to identify an “unknown” gene and then determine conservation of this gene, disorders/symptoms caused by mutations in this gene, and gene locus on the map viewer.

The NCBI contains a database of genes from multiple organisms that have been sequenced and identified. The work of a number of scientists across a wide variety of research areas provides the information compiled in this database. BLAST - Basic Logical Alignment Search Tool - allows a user to submit a sequence of nucleotide bases into the search engine; BLAST will search the database and find the gene associated with that sequence. Furthermore, the user can access information about the gene or the disease it causes.

This activity is adapted from Stephen Wefer's Name That Gene found in American Biology Teacher, Vol 65, No.8 Oct 2003.

Grade Level: 

Concepts Covered: 

Genetics, DNA Sequence, Gene Locus, BLAST analysis

Prior Knowledge Required: 

Gene, Locus, Phenotype, Nucleotide

Activity Notes

Days to Teach: 

1-2 days

Materials: 

Computer Access

Teaching Tips / Activity Overview: 

  1. Post the student handout BLAST that Gene online so that students can access the paper from their mobile devices.  This will allow them to copy and paste the sequences faster than having someone dictate the sequence.
  2. Introduce the activity and have the students do the Pre-Lab section.  Review the answers with the class.
  3. Have students work individually or in small groups to complete the rest of the activity.

 

  • Check the BLAST site before handing out the link to the activity.  This site is a dynamic site and is constantly changing so the directions on where to find links and the screen shots may need to be adjusted.    
  • Have students check with each other before coming to you for direction on where to click next.  This will help them find some independence and enable you to help more students.

Assessment: 

Proper identification of gene/disorder

Extensions: 

  • Students can search for more gene sequences of their choosing or they can find a DNA sequence associated with a gene/disorder and BLAST this sequence to find more information about it. 
  • Student Debate:
    • Should insurance companies have access to individual’s DNA sequences before they agree to insure them? Should genomic information be given to your doctor?  Employer? Future spouse? For a peek into your genetic makeup?  Do the benefits of some scenarios outweigh the potential costs?  Students explore sources supporting and opposing the use of Genomic DNA Sequencing for disorders, then hold a classroom debate to decide whether this technology should be used to peek into someone’s potential future.   

 

Resources: 

  • NCBI— (http://www.ncbi.nlm.nih.gov) A suite of interlinked bioinformatics databases that detail DNA, protein, gene and disease data.
  • OMIM—Online Mendelian Inheritance and Man (http://www.ncbi.nlm.nih.gov/omim) An extensive medical database of human disease phenotypes and associated genes.
  • MapViewer—(http://www.ncbi.nlm.nih.gov/mapview) Used to visualize genetic, physical, gene and other maps.
  • BLAST—Basic Local Alignment Search Tool (http://blast.ncbi.nlm.nih.gov/Blast.cgi) aligns a protein or nucleotide (DNA) sequence against the billions in the database to look for matches.  Can be used to find difference between sequences, or to look for similarity between known sequences.  BLASTn compares nucleotide sequences.  BLASTp compares protein sequences.

Acknowledgements: 

Adapted from: Wefer, Stephen  Name That Gene  American Biology Teacher Vol 65, No.8 Oct 2003.  The teacher notes and handouts are compiled from lessons produced by Rachel Stern and Jason Ambler.

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