Multiple Sequence Alignment using CLUSTAL W

 

Multiple Sequence Alignment using CLUSTAL W

Aim

To show phylogenetic relationships of sequences by creating tree.

Description

Multiple sequence alignment is simply an alignment that contains more than two sequences. Multiple sequence alignment is very important for finding similar domains in a set of sequences and further doing phylogenetic analysis. There are two methods of multiple sequence alignment; progressive and iterative. CLUSTAL W is an example of progressive method. It produces multiple sequence alignment of divergent sequences. Evolutionary relationships are shown through cladogram.

 

Procedure

STEP 1: Obtain sequence from NCBI for multiple sequence alignment. Go to NCBI homepage, select nucleotide/protein database and type the query. Select the hit in FASTA format for similarity search.

STEP 2: Select BLAST-n option from NCBI -BLAST

STEP 3: Run BLAST.

STEP 4: Select three or four sequence similar to query and download it in FASTA format.

STEP 5: Go to https://www.genome.jp/tools-bin/clustalw

STEP 6: Paste selected input for multiple sequence alignment in the query box

STEP 7: Set up the pair wise alignment parameter

STEP 8: Set up multiple sequence alignment parameter

STEP 9: Click Submit button

STEP 10: Save the result

STEP 11: Close the window

 

Result

Rooted phylogenetic tree(Maximum likelihood)            

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