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EBI 2Can Tutorials Protein and Proteomic Analysis

2Can Support Portal - Protein and Proteomic Analysis

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

Running a ClustalW2 alignment


We will consider aligning the several myosin heavy chain proteins, represented by the accession numbers below.

Q9Y623  P02562  Q28641  Q9Y622  Q9UKX2  P13535
P02565  P13538  P12847  P11055  Q90339  P12883
P13540  P79293  P02564  P02563  Q02566  P13539
P13533  Q9UKX3  P29616  P05661  P24733  P02566
P04462  P12844  P02567  P11778  P12845  Q05000
P10567  Q02171  P13392  Q01202  P35418  P35417
Q05870  P35415  P06198  P13541  O08638  P35749
P10587  P35748  P35579  Q62812  Q9JLT0  P35580
P14105  Q27991


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

 
>sequence1
NRALSAELQSVTEQLSDGGKNSAEVEKLRRKLGMENEELQIALEEAEAALEQEEGKLLKV
QLEYTQLRQSSDRKLSEKDEELEGLRKNHQRQMESLQNTIDSESRSKAEQQKLRKKYDAD
>sequence2
MMELESQLESSNRVAAESQKQMKKLQAQIKELQSMIDDESRGRDDMRDSASRSERRANDL
AVQLDEARVALEQAERARKLAENEKSENSDRVAELQALYNNVANAKAEGDYHSLQEEIED
>sequence3
LENEAKASEDKAQRAMAEVARLMSELNSAQEATSTAEKSRQLVSKQVADLQSRLEDAEAQ
GGKGLKNQLRKLEQRIMELESDVDTEARKGADAIKAARKSEKKVKELAFTIEDEHKRREP


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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