Adapted from Stephen H. Wefer, "The American Biology Teacher"
Objective: In this activity you will use the website for the National Center for Biotechnology Information to identify a sequence of bases from a DNA sample.
Background: The NCBI contains a database of genes sequenced and identified. The work of a number of scientists and a wide variety of areas allows for information to be compiled into this database. The tool used in this activity is BLAST - Basic Logical Alignment Search Tool, which allows a user to submit a sequence of DNA bases (A, T, G, C) into the search engine, BLAST will search the database and find the gene (if any) associated with that sequence. Furthermore, the user can access information about the gene or the disease it causes.
Open the data page to type in your data as you go.
You will be given a nucleotide sequence found in real human DNA that is associated with a genetic disease when mutated. Your job is to compare the sequences you are given with the nucleotide sequence of most known genes, using the BLAST tool to search genetic databases.
1. Connect to the internet.
2. Find the homepage for NCBI ( www.ncbi.nlm.nih.gov)
3. Click on the word "BLAST" located in the blue bar at the top of the page.
4. Scroll down until you find the heading "Nucleotide-nucleotide BLAST" and click on the link.
5. Type the exact nucleotide sequence you are given in the large empty box. Accuracy is important! It may be helpful to have your lab partner read the sequence in threes. (OR just copy/paste from this page)
6. When you have finished entering your sequence, click on BLAST. On the next screen, click on the "Format" bar. You will then see a screen asking you to wait 10-20 seconds, be patient while formatting takes place.
7. After the search has ended, scroll down the screen until you find the words "Sequences Producing Significant Alignment". Listed in order are the closest matches with your DNA sequence. Click on the blue reference number preceding the first listing (the closest match). This will tell you the name of the gene and its abbreviation (if available).
8. Once you have identified the gene, close the search page and return to the NCBI Home Page
9. In the right hand column, click the link "Genes and Diseases"
10. Across the top of the page, you will notice the numbers 1-22 XY. These numbers represent the chromosomes found in humans. Click on each number to locate the position of your gene on a chromosome.
11. Click on the name or abbreviation of the gene on the chromosome in order to find out the effects or symptoms produced by the defective gene.
12. Fill out the attached data sheets, print and turn in.
Gene Sequences: Your teacher will assign you 2-3 of the following sequences to BLAST - Use copy/paste to save time.
Gene Sequence 1
ATG GCG ACC CTG GAA AAA GCT
GAT GAA GGC CTT CGA GTC CCT CAA GTC CTT CCA GCA GCA GCA GCA
GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GC
Gene Sequence 2
ATG GCG GGT CTG ACG GCG GCG
GCC CCG CGG CCC GGA GTC CTC CTG CTC CTG CTG TCC ATC CTC CAC
CCC TCT CGG CCT GGA GGG GTC CCT GGG GCC ATT CCT GGT GGA GTT CCT GGA GGA GTC TT
Gene Sequence 3
ATG CTC ACA TTC ATG GCC TCT
GAC AGC GAG GAA GAA GTG TGT GAT GAG CGG ACG TCC CTA ATG TCG
GCC GAG AGC CCC AGC CCG CGC TCC TGC CAG GAG GGC AGG CAG GGC CCA GAG GAT GGA G
Gene Sequence 4
ATG TTT TAT ACA GGT GTA GCC
TGT AAG AGA TGA AGC CTG GTA TTT ATA GAA ATT GAC TTA TTT TAT
TCT CAT ATT TAC ATG TGC ATA ATT TTC CAT ATG CCA GAA AAG TTG AAT AGT ATC AGA TTC CAA ATC T
Gene Sequence 5
ATG CGT CGA GGG CGT CTG CTG
GAG ATC GCC CTG GGA TTT ACC GTG CTT TTA GCG TCC TAC ACG AGC
CAT GGG GCG GAC GCC AAT TTG GAG GCT GGG AAC GTG AAG GAA ACC AGA GCC AGT CGG GCC
Gene Sequence 6
ATG CCG CCC AAA ACC CCC CGA
AAA ACG GCC GCC ACC GCC GCC GCT GCC GCC GCG GAA CCC GGC ACC
GCC GCC GCC GCC CCC TCC TGA GGG ACC CAG AGC AGG ACA GCG GCC CGG AGG AC
Gene Sequence 7
ATG TTG TGCAAT ATC CAT CTA
CTG TAG TTA AGA TAT TCA GTA GTT TGT TTT TCA TAA GCA TGT AAT
TGA TCA TAT TTC TGC CAA GGA TGT GCC TTC AAC TTT ATA ATT ATA GTG TTG TAA AAT ATT TTT GTC TG
Gene Sequence 8
ATG CCA TCT TCC TTG ATG TTG
GAG GTA CCT GCT CTG GCA GAT TTC AAC CGG GCT TGG ACA GAA
CTT ACC GAC TGG CTT TCT CTG CTT GAT CAA GTT ATA AAA TCA CAG AGG GTG ATG GTG GGT GAC CTT