Steps to perform multiple sequence alignment:

 

To download the data , and to get acces to the tools, go to simulator tab.

 

Get access to the CLUSTALW tool 

 

Figure 1: Screenshot of the CLUSTALW tool

 

In the dialog box given, paste your set of sequences, the sequences should be pasted with the ‘>’ symbol followed by name of the sequence (as similar as FASTA format) followed by return (enter key) and then the sequence (Figure 2).

 

 Figure 2: Screenshot to paste the sequence for alignment

 

The sequences can also be submitted through file by clicking on the option “choose file” such that all the sequences should be in similar format.

 

The other two steps the user can select on his/her own to set the parameters for pair wise alignment options and multiple sequence alignment options, to select the scoring matrices and scoring values. In most of the cases the parameters are set default (Figure 3).

 

Results can be notified by email when the user checks the button email notification (Figure 3).

 

 Figure 3: Screenshot of the Parameters to be submitted for the alignment

 

 

After the submission of the job the results can be downloaded into a file by clicking on the option Download alignment file (Figure 4).

 

Figure 4: Screenshot to download the alignment file

 

The result summary tab gives the links to different outputs summary and link to each output (Figure 5).

 

Figure 5: Screenshot of the Results summary

 

The  result files are with different formats of input and output files of the alignment.

 

The user can enable the java plug-in in the browser, if it is disabled and thus the user can use Jalview to see the alignment with the colours as shown in Figure 6.

 

 Figure 6: Screenshot of Jalview

 

The user can view the output file and can save by clicking on the button “View output file” as shown in Figure 5.

The output file represents the length of each sequence , and the score of each alignment individually  as shown in Figure 7.

 

 Figure 7: Screenshot of the output file to be saved

 

 

 

This Experiment uses:  EMBL-EBI  CLUSTALW,    http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_rest  and  National Center for Biotechnology Information (NCBI) ,  www.ncbi.nlm.nih.gov