BLASTing flu viruses

[deleted-92474]

Okay,so basically,my question is: How can I get the full 566 amino acid sequence for the hemagglutinin protein of the flu strains?
The project page said this in regard to that:

Full-length HA is 566 amino acids. In order to retrieve full length-entries, add this text to the search box AND 566[SLEN]. Click "Go."

I tried doing it,but all that GenBank says is "No items found."
Can someone help me?

[carolinethorn]

Hi,

In order to help you trouble shoot we need some more details about what exactly you did.
Which strains of flu are you trying to retrieve? Maybe you had a typo in the name of the strain you chose?
What happens if you try the test example "A/Wisconsin/67/2005 AND 566[SLEN]" does that work?
did you take out the quotation marks? (i forgot to do this when i tried it and it didnt work)
did you remember to select protein on the pull down menu?

Have another try and keep track of exactly what you did if it doesn't work so we can help you.
Good luck,
Caroline

[deleted-92474]

Well,I did the A/Wisconsin/67/2005 AND 566[SLEN] thing, and it worked, but when I tried it with the strains I needed, it's still "No items found".
I am trying to retrieve:
A/New Caledonia/20/99
A/Solomon Islands/3/2006
A/Brisbane/59/2007

I didn't put quotation marks,and I'm on the Protein page.
Thanks for trying to help.

[carolinethorn]

Thanks for the extra info. It enables me to go and try doing what you are doing and see why it might not get the expected result.

I searched A/New Caledonia/20/99 AND 566[SLEN] and as you found nothing comes up.
This is a very specific search for the full length hemagglutinin. Maybe no one has published the full length hemagglutinin protein from this strain. So I tried just searching for any hemagglutinin proteins from A/New Caledonia/20/99 using the search phrase "A/New Caledonia/20/99 hemagglutinin". This gets results that you can scroll down and find the closest to full length one.

Maybe you can't get 566aa length sequences for your strains of interest but you could get the longest possible and align those.

Best of luck,
Caroline