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Global alignment of two sequences - Needleman-Wunsch Algorithm
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Procedure:

The two sequences can be aligned globally using different algorithms. Needleman-Wunsch algorthim is one of the best algorithm for global alignment, which can be performed using the online tool EMBOSS Needle (European Molecular Biology Open Software Suite).

 

Steps to align the Sequences:

 

Step1:

 

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

 

2. Get access to the tool EMBOSS Needle

 

 

 

Figure 1: Screen shot to redirect EMBOSS needle and paste the query sequences for sequence alignment

 

3.Copy and paste the FASTA formatted (Computational representation of the DNA sequence) nucleotide sequence in the step 2 dialog box (as shown in figure 1).

 

4.One can also choose the file through “Choose File” option and can upload the sequence file.

 

5.Similarly copy and paste or upload the second sequence for the alignment.

 

Step 2:

 

1.EMBOSS needle is predefined with the scoring matrices DNAfull for nucleotide sequence, BLOSUM65 for protein sequence (Figure 5).

 

2.The gap open and gap extend penalty can be changed by user defined values. In this example it kept as default values.

 

3.The user can be notified with the results through email, if the checkbox is checked and the mail address is submitted.

 

 

Figure 2: Screenshot to set the parameters for the pairwise sequence alignment using Needleman –Wunsch algorithm

 

Results

 

After the job is submitted by clicking on the submit button, the results are displayed within few minutes. The Results page comprises of three tabs namely Alignment, Submission details and submit another job.

 

The Alignment tab shows the alignment of the two sequences, with all the described parameters, used scoring matrices and Gap penalty scored values.

 

The Alignment tab has an option for the user to download the entire alignment file by clicking on the button “View Alignment File” (Figure 3).

 

 

Figure 3: Screen shot to show the result of pair wise sequence alignment with different tabs

 

The alignment between the two sequences is shown in Figure 4, the gaps are represented with ‘-‘. If a match is there between the two nucleotide there is a symbol ‘|’ and the mismatch is represented with a dot ‘.’

 

Figure 4: Screenshot explains the Alignment of the two sequences

 

The submission details tab displays user to show the program used, time and date of when the program has launched and the internal commands used for the program execution. Also the user can download the input and output files from this tab (Figure 5).

 

Figure 5: Screenshot of the submission tab details

 

  

 

This Experiment uses: EMBL-EBI EMBOSS needle, www.ebi.ac.uk/Tools/webservices/services/psa/emboss_needle_rest and National Center for Biotechnology Information (NCBI) , www.ncbi.nlm.nih.gov

 

 

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