Creating Multiple Sequence Alignments
In this example, we will create an alignment from
protein sequence data that will be imported into the alignment editor using
1.0.1: Start MEGA by double-clicking
on the MEGA desktop icon, or by using the Windows start-menu to click on the
MEGA icon located in the programs folder.
1.0.2: Launch the Alignment Explorer
by selecting the Alignment|Alignment Explorer/CLUSTAL menu command.
order to align sequences contained in a Sequence Data File, do the following:
1.1.1: Add unaligned sequences from
the hsp20.fas example file into the Alignment Explorer by clicking selecting
Sequences from File menu command.
1.1.2: Select the Edit|Select All menu command to select every site for all sequences in the
1.1.3: Select the Alignment|Align by ClustalW
menu command to align the selected sequences data using the ClustalW
1.1.4: Save the current alignment
session by selecting the Data|Save Session menu item. This will allow the
current alignment session to be restored for future editing.
1.1.5: Exit the Alignment Explorer by
selecting the Data|Exit Alignment Explorer menu item.
A message will appear asking if you would like to save the data to a MEGA file.
Choose “YES,” and then a “Save As” dialog box will appear. Enter
hsp20_aligned.meg as the file name, and click the “Save” button. An input box
will appear asking for a title for the data. Enter “HSP 20 Aligned by MEGA” as
the title, and click the “OK” button. Another dialog box will appear asking you
if the sequence data is protein coding. In this case, click “Yes.” A final
dialog box will appear asking you if you would like to open the data file in
MEGA. Click “Yes.”
Now, we will examine how to send sequence data from the Internet (Web
Explorer) to the Alignment Explorer.
1.2.1: If the Alignment Explorer
already contains sequence data, select the Alignment
| Create a new alignment menu command to create a new alignment. Choose
“YES” on the dialog box that appears to indicate that you are creating a DNA
1.2.2: Activate the Web Explorer tab
by selecting Web|Query Gene Banks from the menu.
1.2.3: When the NCBI Entrez site is loaded, select either
the nucleotide or protein database, enter a search term into the search box,
and press the “GO” button.
1.2.4: When the search results are
displayed, select the specific search item and choose “Sequence” from the menu
bar. Press the “Add to Alignment” button located to the left of the address
box. This will display the Web Fetch dialog window.
1.2.5: Click the box to the left of
each accession number whose sequences’ information you would like to fetch from
the web. When you are done, select accessions by pressing the
1.2.6: When the status column
indicates that all sequences are fetched, press the “Send to Alignment” button
to send the fetched sequence data to the Alignment Explorer.
1.2.7: Align the fetched data using
the steps detailed in Ex 1.1.2 – Ex 1.1.5.
may also open a trace file in the Trace
Data Viewer/Editor and send it directly to the Alignment Explorer.