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Smith-Waterman Algorithm - Local Alignment of Sequences





The two sequences can be aligned pairwise using different algorithms , Smith-Waterman algorthim is one of the best algorithm , which can be performed using the online tool EMBOSS water.


Steps to perform alignment


Step 1:

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


1. Get access to the tool EMBOSS Water


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


2.Copy and paste the FASTA formatted (Computational representation of the DNA sequence) nucleotide sequence in the step1 dialog box (as shown in Figure 1).


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


4.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 2).


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 results through email, if the checkbox has been checked and the mail address is submitted.



Figure 2: Screenshot to set the parameters for the pair wise sequence alignment using Smith –Waterman algorithm




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 specified details like 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 water, www.ebi.ac.uk/Tools/webservices/services/psa/emboss_water_rest and National Center for Biotechnology Information (NCBI) , www.ncbi.nlm.nih.gov


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