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ClustalW is a popular multiple sequence alignment program that allows you to detect similarities and differences among submitted DNA or protein sequences. Its position-specific scoring scheme and down weighting of over-represented sequence groups facilitate the generation of biologically meaningful alignments. The tool is often used as part of an analysis pipeline to predict the functions and structures of proteins and to identify new members of protein families.

See also: Help:BLAST Search, Help:InterProScan


Using ClustalW

There are three entry points to run ClustalW in the wiki as described below. Both methods will submit the input sequences to the European Bioinformatics Institute (EBI) for analyses through Web services.

On a protein page

If a protein has more than one sequence variant, click on the Tools tab on the right of the page, and the "Align All Isoforms" link will appear, with which you can readily submit all of the sequences for alignment using ClustalW.

See also: Help:Salivary Proteins

On a protein cluster page

If there is more than one member in a protein cluster, the "Align All Cluster Members" link will appear in the Tools panel. Clicking this link will submit the canonical sequence of all the cluster members to ClustalW.

See also: Help:Protein Clusters

Using the ClustalW special page

The interface on Special:ClustalW gives you the flexibility to run alignment on any protein sequences of your choice. On each line of the text box, enter the page title of a protein sequence stored in the wiki (e.g. HSPW:PDDBCB3/1), and the tool will run the analysis on sequences extracted from the specified pages. Alternatively, you can enter the actual amino acid sequence in lieu of a page title if the protein is not currently stored in the database.

Display of Results

Once the analysis is finished, the server at EBI returns the results in text format. To help you visualize the alignments more easily, the wiki provides you access to Jalview, a sequence alignment editor. Simply press the Start Jalview button on top of the result page to launch the applet (see Fig. 3). In addition to viewing the alignments, there are also other tasks that you can perform within the editor. Principal component analysis and tree generation are some of the examples. For more information about using Jalview, see this Jalview Quickstart Guide.

Multiple sequence alignment using ClustalW
Fig. 1: Sequence alignment results of protein cluster members visualized in Jalview.


1.Thompson JD, et al. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22):4673-80 [PubMed:7984417]
2.Clamp M, et al. (2004) The Jalview Java alignment editor. Bioinformatics 20(3):426-7 [PubMed:14960472]
HSPW Version 1.5.3. This page was last modified on 24 August 2011, at 14:30.This page has been accessed 219 times.