Sequence alignment activity

(database) Activity Taken from  American Museum of Natural History online course:  Evolution

1. 1.
   

1. a)Go to the web-site of the National Center for Biotechnology Information
   

2. b)Choose ‘gene’ from the search menu
   

3. c) Enter a gene plus the organism such as cytochrome oxidase 1 (COX1) for pan (chimpanzee).

   

   
   
4. d)Click on cox 1 and mouse over the section  ‘Genomic regions, transcripts, and products’  until ‘Nucleotide Links’ appears.

   

   
   

2. 
   

5. e)Choose Fast A and the sequence should appear.  Copy the sequence and paste it into a .txt file or notepad file
   

6. f)Repeat with a number of different species that you want to compare.
   

7. g)

   

   
   

8. h)If you want the students to have the computer align the sequence download the software called ClustalX
   

9. i)Save the file of all the different sequences as sequences.fasta
   

10. j)In the File menu, choose Load Sequences.
    

11. k)Select your file. Your sequences should show up in the ClustalX window.
    

12. l)Under the Alignment menu choose Do Complete Alignment.