- Multiple Sequence Alignment (MSA) with ClustalW2 and MuscleThe final workflow after the execution and some results.
5 steps required
Step 1. Open a new
Open the File Menu
When asked if you want to migrate your data and workflow to the new
project, select NO.
Then, enter a new project
For the time being, we will be working with the default name.
The new project
file (New_Untitled.db) will be in the \projects\ directory.
Step 2. Insert a new
Go into the File Menu
the Import Sequences
Select the file hiv.fasta
A new dialog box will be shown where you can enter some informations
about the sequence files, type of sequences (DNA, RNA or AA [Amino Acid]).
when you''ve finished entering informations.
Note: The name prefix will be added to all files. It allows for a simplified loading of multiple sequence alignment files.
Once imported, you can find the newly imported MultipleSequences
the Workflow Database
pane. (Note: the name of the MultipleSequences might be different).
To use it, "drag and
the new MultipleSequences object into the Workflow
area (see below
Step 3. Add the MSA
Go into the Workflow Tools
and using the same "drag and drop" motion, add the ClustalW
application to the Workflow
Note: Executing this workflow locally can be SLOW.
If you have Internet access, you can use the ClustalW2 (Web EBI) and
Muscle (Web EBI) applications instead, which result in a running time
of ~7 minutes for this HIV dataset.
To speed up the analysis, open the Muscle
configuration box by Double-Clicking
with the left mouse
button on the Muscle application box and select in the "Fast setting" the "Fastest possible (nucleotides)
with the left mouse
button on the Red dot
(identifying the application data output
s) to show all application outputs.
Note: The blue color
any input or output data indicates that either it is undefined or has not
been generated. Once the data are genetated, the output will
turn to the green color
, as shown below.
Connect the MultipleSequences
to the applications box by selecting
the connection box
at the end of the MultipleSequences object and link it to each of
the multiple sequence alignment applications (i.e. ClustalW2 and
Step 4. Execute the workflow
In the far right corner of
the worflow artea, click on the Run
While the applications are running you can see the application
progress either by looking at the workflow progress bar (above the workflow area) or by clicking
on the Output
panel (see below).
You can save
this generated application output to a text file by clicking
on the bottom-left button "Save as Text"
When all the workflow executions have been carried out, a
should appear on the right-corner of each application box. If an error has occured, a warning sign
will be displayed.
Step 5. Display the results
To view a Text View
of the multiple sequence alignment, either double-click
on the application
aligment output or right-click
on it and select "View"
In this view (see below), you can select either a
simplified representation of the aligned sequences, or a
fasta or phylip format for rapid "Cut-and-Paste
" to other applications.
To display a more graphic representations, right-click on the aligment output and select "View Graphic"