First, study the above Terms and Concepts. It's especially important that you research and understand flu notation.
How to retrieve the protein sequence for hemagglutinin in strains of influenza used as vaccines, and BLAST it. 1. Go to the Flu Activity & Surveillance page at The U.S. Centers for Disease Control and Prevention (CDC) website: www.cdc.gov/flu/weekly/fluactivity.htm. 2. Open a new page that has information about past flu seasons. Click on "Go" next to the year of choice. For example, click on "Go: 2006–2007 Influenza Season Summary." 3. Read the information on the page. o In particular, find the paragraph with the heading "COMPOSITION OF THE 2006–07 INFLUENZA VACCINE": o It will tell you the name of the virus strains that were selected for use as vaccines. For example, "The Food and Drug Administration's Vaccines and Related Biological Products Advisory Committee has recommended that the 2006–07 trivalent influenza vaccine for the United States contain A/New Caledonia/20/99-like (H1N1), A/Wisconsin/67/2005-like (H3N2), and B/Malaysia/2506/2004-like viruses." 4. You can obtain the sequences for these strains from the NCBI GenBank website: www.ncbi.nlm.nih.gov/Genbank/. 5. Select "Protein" with the “Search” drop-down menu. o Type in the name of the flu strain in the search box. o For example, copy and paste "A/Wisconsin/67/2005" into the box near the text "search for." o Full-length HA is 566 amino acids. In order to retrieve full length-entries, add this text to the search box AND 566[SLEN]. The search text in this example is "A/Wisconsin/67/2005 AND 566[SLEN]." o Click "Go." 6. Click on the active link for the HA protein page. See this example. 7. Copy the accession number for the full-length HA protein. 8. Click on the "BLAST Sequence" link (column on right side of page). 9. The BLAST page will pop up. The database should be set automatically to "non-redundant protein" and the algorithm should be "blastp." 10. Click the BLAST button.