Getting started with Sim4 tool: Nucleotide Sequence Alignment 

Author Name : C.P.Rajadurai

Mail ID : rajaduraicp_at_au-kbc.org


Sim4 is a tool for doing pairwise alignment to find the similarity between nucleotide sequences. 

Step: 1 

Download raw nucleotide or protein sequence from nucleotide database and save it

in a folder as a separate directory. Change the directory by using the command

cd your-directory-name. List the downloaded files by using ls command. 
 

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Step: 2 

Change the directory, type sim4 and press enter.

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Step: 3

 

Type sim4 NucleotideSequence1.txt NucleotideSequence2.txt and press enter. 

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Step: 4 

The result shows that how much percentage of identity of the subject sequence with your query sequence. 

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Step: 5

We can also do alignment with multiple sequences with your query sequence by giving the command sim4 nucleotidesequence.txt multiplesequence.txt and press enter. 

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