Introduction to BLAST

Assignment Goal: To use the Internet-based site BLAST, Basic Local Alignment Search Tool (NCBI), to search for similarities between nucleotide sequences.

Assignment: Access the BLAST site at http://blast.ncbi.nlm.nih.gov/Blast.cgi

Click on “Nucleotide Blast”

Assume that you found this nucleotide sequence when you cloned a piece of gene in the laboratory in which you work: 

aattggaagc aaatgacatc acagcaggtc agagaaaaag ggttgagcgg caggcaccca gagtagtagg tctttggcat taggagcttg agcccagacg gccctagcag ggaccccagc

Enter the above sequence (you may copy and paste) into the “Enter Query Sequence” box at the top of the page. Under “Program Selection” near the bottom of the page, choose “somewhat similar sequence (blastn)”

Click the “BLAST” button at the bottom of the page to run the search.

Give some time for the results of your search to show up.

You will be given significant matches for the sequence that you entered.

6. WHAT IS THE TOP SEQUENCE DESCRIPTION MATCH FOR YOUR QUERY SEQUENCE?  For this answer, you should give the description listed. Do not choose a Predicted sequence.

7. WHAT DOES THE ENCODED PROTEIN DO IN THE BODY? Search the PubMed site at www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed to answer this question. Under “Article types,” choose “Review”. CITE THE PAPER YOU USED TO DETERMINE THE PURPOSE OF THE ENCODED PROTEIN.

Click on the top match to find the following.

8. FOR WHAT DISEASE IS A MUTATED FORM OF THIS GENE RESPONSIBLE? You should be able to get this information from the description of the gene.

9. ON WHAT CHROMOSOME IS THE GENE LOCATED? You should be able to get this information by clicking on the description of the gene.

10. Return to the original nucleotide sequence alignment descriptions. WHAT SPECIES (STATE THE SCIENTIFIC NAME) OTHER THAN HOMO SAPIENS ALSO HAS A 100% IDENTITY (Ident) FOR THIS SEQUENCE?

11. WHAT IS THE COMMON NAME FOR THIS SPECIES?

12. DOES IT SURPRISE YOU THAT THIS SPECIES ALSO HAS A 100% SIMILARITY IN IDENTITY? WHY OR WHY NOT?

13. DESCRIBE THE FIRST MATCH THAT HAS LESS THAN 100% QUERY COVER. STATE THE SCIENTIFIC AND COMMON NAMES.

14. Click on the description to answer this question. HOW MANY GAPS OCCUR BETWEEN THE TWO SEQUENCES (THE ONE YOU SUBMITTED AND THE FIRST ONE THAT HAS LESS THAN 100% QUERY COVER)? 

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