BLASTing Flu Viruses

[swimmy]

Thank you so much!

[InfluenzaScienceFair]

Hello,

I have had similar problems with this project. Many of the prior posts have helped me a lot, but I still am kind of confused. My question was "Based on a certain year’s influenza outbreaks, how effective are the vaccines for the following year?" Is that reasonable?

[MelissaB]

HI,

I'm not sure what you mean by, 'based on a certain year's influenza outbreaks'. What about those outbreaks will you measure? Strength of the flu season? Viral sequences? If you can explain it a bit more, I might be able to help you.

[swimmy]

In BLAST, is there any way to limit the query to America?
The CDC has information about the cases in America, but the BLAST has strains from around the world...
Also, is there anywhere that says how many vaccines were administered?

[InfluenzaScienceFair]

I was thinking of the viral sequences, yes. Since the vaccine for the following year is composed of the most prominent sequences from the prior year's outbreaks, I wanted to find the percentage of effectiveness in the vaccine. I don't really know if that makes sense, but it was just a thought.

[MelissaB]

Swimmy,

I know of no way to limit the search to America--but the good news is that the flu is pretty pandemic, so the sequences you get are likely to have pretty much been around the world. As for the doses, I couldn't find exact doses, but I found percent coverage of different groups (those 65 and older, those 18-41 with certain risk conditions, etc.) here: http://www.cdc.gov/flu/mmwrref.htm .

ISF,

That's certainly do-able, but you'll find that it varies widely from year to year--some years the last seasons' sequences work very well, and some (like this year!) they work very poorly. I would thus suggest having another variable, or considering a different question.

[InfluenzaScienceFair]

All right, thanks! So if I do choose to do that question, how would I be able to find the percentage of effectiveness?

[swimmy]

I'm trying to see how similar the sequences are.
Do I use Identities, Positives or Gaps?
I found this in the BLAST tutorial:

Similarity
The extent to which nucleotide or protein sequences are related. The extent of similarity between two sequences can be based on percent sequence identity and/or conservation. In BLAST similarity refers to a positive matrix score.

I don't really understand. I think I use the positives to find the similarity.
Is this right?

[MelissaB]

Hi guys,

I'm so sorry that no one has answered your questions yet! ISF, I hope that you have figured out that I talked about how to measure effectiveness earlier in the thread? If not, let me know and I'll help you out with that.

Swimmy, I'm no expert in BLAST, but I just looked it over and I think you should use identities. That seems to be the number of nucleotides the two sequences have in common divided by the total number of nucleotides. The percentage you get after is the percentage similarity.

[MichaelD]

I'm trying to see how similar the sequences are.
Do I use Identities, Positives or Gaps?
I found this in the BLAST tutorial:

Similarity
The extent to which nucleotide or protein sequences are related. The extent of similarity between two sequences can be based on percent sequence identity and/or conservation. In BLAST similarity refers to a positive matrix score.

I don't really understand. I think I use the positives to find the similarity.
Is this right?

Yes that is correct. The positives will indicate residues which are similar (homologous) in properties, acidic, basic, hydrophobic, etc. Identities indicate an exact match. Percent positive will be a good measure of similarity between two sequences.

Mike