In this exercise we will perform a multiple alignment using a program called ClustalW at Baylor College Medicine (BCM) Molecular Biology Server.
ClustalW is perhaps the best known multiple alignment program and is available at a number of sites. You can also download versions that will run on your own computer.
Step 1: In this exercise we will align protein sequences of the enzyme alcohol dehydrogenase from 4 different organisms. Click here to bring up the sequences in a window. Copy the entire set of sequences to the clipboard.
Note that the protein sequences are in FASTA format (What is FASTA format?)
Step 2: Launch the BCM ClustalW web tool by clicking here
Paste the protein sequences in the large text box. Notice you can get the results emailed back to you if you wish – in this case we’ll just get them back on the screen.
Make sure ClustalW 1.8 is selected as the alignment method.
Leave all the other parameters as they appear, but notice the range of other possible options on this page.
Click on the grey submit button to start the alignment. (show me)
Step 3: After a short delay you will now be presented with the results page for the alignment of these four protein sequences.
Although this format may be sufficient it would be nice if it was easier to see theconserved amino acids.
We will use the program boxshade to may the output from ClustalW look prettier.
Copy the text contained within the green shaded region to the clipboard. (show me)
Click here to launch the Boxshade tool.
Step 4: Scroll down the page and paste the sequence that you copied to the clipboard in step 3 into the box labelled ‘Paste your multiple-alignment file’.
Change the drop down list labelled ‘output format’ to read ‘RTF-new’ to allow us to view the results using Word. Note the wide range of other output formats.
Change the drop down list labelled ‘Input sequence format’ to ‘other’
Leave all the other options as their default settings for now, but note the possible range of other options.
Click on the grey button labelled ‘Run BOXSHADE’ to start the process. (show me)
Step 5: You will be presented with a green BOXSHADE results screen that contains a link to your finished alignment.
The alignment is not viewable on the web page, we need to download it as a file to open in Word.
Click on the link labelled ‘here is you output number’. (show me)
What happens next depends on which web browser you are using. You may be prompted with a dialogue box asking you whether you want to open the file or save it. Save the file to your filespace somewhere convenient. The file may be viewed by opening it in Word.
In some browsers the file will be opened and the shaded alignment will appear on the screen. You may then save it as a Word file by using the save as option on the file menu of the browser.