In this section you will compare sequences by aligning their residues using CLUSTALW.

In order to compare two nucleic acid sequences they must be alligned one on top of the other.  This is the purpose of the CLUSTALW tool.  The alignment process  performed by CLUSTALW compares the two sequences and finds the common regions within them; it actually computes the most likely position in which the two sequences line up.  Once the two sequences are aligned, a color coding system is used to differentiate highly conserved regions and semi-conserved regions (in royal blue and green, respectively) from the non-conserved regions.
Therefore, sequence alignment is a key step for you to determine where a mutation is located.

Click to run a video demo of all the steps described below. In order to play the video, you should have flashplayer plugin installed. You can download the plugin from

1.  Choose the sequences to align. In this case two sequences:
Select the wild type geta-globin gene identified as GBPRI:29436
Select the mutant gene identified as GBPRI:183944

2.  Choose the aligning programs.
Scroll down the window and highlight the program
CLUSTALW - Mutiple Sequence Alignment
Click on the Run button

3.  Select the CLUSTAW parameters.
The previous step takes you to the parameters page for the CLUSTALW program.
Do not change any of the parameters on this page.
Scroll down the page and click on the Submit button.

4.  Examine the aligned sequences.
The screen of the results of running CLUSTALW  has several parts.
The section near the top of the screen displays the input sequences you provided
The next section of the screen shows the list of commands that you can run on the data that appears on this screen; namely: Import Alignment(s), Return, Help, Report Bugs.
The next section starts with the title Sequence alignment and shows the details of the result of running the CLUSTALW program.
The alignment itself is structure as follows: there is a line for each sequence and then there is an additional line for the consensus sequence. 
The line will display up to 60 residues; if either sequence is longer than 60 residues; then   it will be split into groups of 60 residues until all the contents of the alignment has been displayed.
The next section of the screen shows the dendrogram
The next section of the screen provides statistics and diagnostic messages generated by     the program CLUSTALW
The next section shows (again) the list of commands
The last section of the screen is for the citation of the algorithm

5. Locating the site of the mutation. 
You will see that GBPRI:29436 has a long string of nucleotides at the beginning, but there are only dashes (----) for GBPRI:183944.  This is a result of the alignment process and the dashes represent gaps in evolutionary terms; that is, there are missing residues from a sequence.  The GBPRI:29436 sequence is longer than GBPRI:183944, so the alignment tool had to slide the GBPRI:183944 sequence down to line them up.  All nucleotides that are colored blue are identical in both sequences and you can see that, as expected, all but a few of the nucleotides are blue.  The important part of the sequence is in the eighth row down.  If you count down 8 lines you will find one nucleotide that is not the same in both sequences.  In the wild type sequence there is a thymine (T), whereas the mutant sequence contains an adenine (A).  This is where the mutation that causes sickle cell anemia has occurred.