CLUSTALW Multiple Alignment of Myoglobin Homologs
CLUSTALW is an aligning algorithm. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.
The results are displayed as sequences of letters. If proteins are being aligned, each letter represents a different amino acid.
Click on the thumbnail to see full-size!The sequences returned to the Biology Workbench "Protein Tools" page from the BLASTP output should be displayed with check boxes in front of them. A multiple alignment (line up the selected sequences) is performed to compare their similarity: Click on the check boxes of approximately 10 sequences to select them.
In the scroll box find CLUSTALW, select it and click on "Run".
Click on the thumbnail to see full-size!A page which says "CLUSTALW - Multiple Sequence Alignment" will open which shows all the sequences which have been selected for multiple alignment. Below this are boxes for setting various parameters. Accept all the default parameters. Click on the "Submit" button.
Click on the thumbnail to see full-size!A box will appear with the alignments returned from CLUSTAL W. A partial view of the first "paragraph" is depicted in the thumbnail to the left. It shows the amino acids at the beginning of myoglobin in each of the species. Each letter is a symbol for a single amino acid. The sequence is color coded according to a complex statistical analysis of similarities.
BLUE Single fully conserved residues. That is, positions at which the amino acids are identical in all sequences. GREEN Conservation of strong groups. Positions at which amino acids are identical in many sequences, and chemically similar in the rest (for example glu and asp; or leu and ile). DARK BLUE Conservation of weak groups. Positions at which the amino acids are not identical, but may share slight chemical similarities in most sequences. BLACK No conservation, identity or similarity. 
Click on the thumbnail to see full-size!Scroll down the output page. The second "paragraph" shows the amino acids in the middle of the protein, and the last "paragraph" shows the last amino acids. Scroll back to the top of the page. Click on the "Import Alignment(s)" button.
Click on the thumbnail to see full-size!You should now have been taken to the Biology Workbench "Alignment Tools" page from CLUSTAL W. The imported sequences should appear in the same format as shown in the thumbnail to the left.
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