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EBI 2Can Tutorials Nucleotide Analysis

2Can Support Portal - Nucleotide Analysis

ClustalW2 multiple sequence alignment <<< 2/6 >>>

Running a ClustalW2 alignment


We will consider aligning the several tropomyosin sequences, represented by the accession numbers below.		 
BF056441 BE8487196 BF022813 BF452255 BG089808 BG147728 BI817778 AF186109 
AF186110 AF310722  AF362886 AF362887 AF087679 SSAJ803 SSAJ804

The sequences for these nucleotides are available here. They are entered in the following format:

 
>sequence1
ATGAAGGATGAGGAGAAGATGGAGATTCAGGAGATGCAGCTCAAAGAGGCCAAGCACATT
ATGAAGGATGAGGAGAAGATGGAGATTCAGGAGATGCAGCTCAAAGAGGCCAAGCACATT
>sequence2
GCAGACGACGCANAGGATCGCGCGCAAGGCCTGCAGCGCGAACTGGATGGCGAGCTCTAG
GCGGACGAGGCAGAGGATCGCGCGCAGGGCCTGCAGCGGGAGCTGGACGGCGAGCGCGAG
>sequence3
GCGGAAGAGGCTGACCGCAAATACGAGGAGGTAGCTCGTAAGCTGGTCATCCTGGAGGGT
GCGGACGAGGCCGAAGAGCGGGCCGAGATCCTGCAGAGGGAGGTGGACGCCGAGAGGCAG

Consider the following ClustalW2 submission form:

Go to the main EBI website
N.B. This tool can also be programmatically accessed as a web service.


  • The multiple sequences were uploaded in FASTA format, which consists of a one-line header starting with a ">" symbol, followed by the sequence name/description. The sequence is then entered on new line(s). Click here to view the input

  • The title of the alignment was changed to mhc align.

  • Other options were left on "default".

We will next look at the results of this ClustalW2 alignment >>>


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