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A few questions about BLASTing Flu Viruses

Postby sez » Tue Dec 11, 2007 8:36 pm

Well since you guys helped me pretty well in my 7th grade project last year I've come again to seek sage advice :D

I've now been researching influenza, its vaccine, playing around with BLAST and the ISD database the last two days to get myself acclimated into all of it. So far it's been *a lot* of new concepts to learn, specially since I'm not taking biology yet. So I've a few questions.

1. What is the difference between the HA and the NA sequence of each virus? Is one the vaccine, and is the other the virus?

2. Where DO you find the sequence for the vaccine? From my understanding, the WHO uses inactivated, "dead" viruses for it. So would they be the same as the virus?

3. Where would be a good place to find a thorough explanation of antigens/antibodies?

4. When the sequence for a virus is put through BLAST, are the closest matches (~100%) the most effective for the vaccine?

5. What is the "Max Score" and the "Total Score" fields in BLAST, using the blastn nucleotide search? Are these basically how many nucleotides from both sequences are the same?

Thanks for any help :)
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Lesson one: Unplus-ing numbers

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n = What I tell you to

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Postby adance » Fri Dec 14, 2007 2:50 pm

Hi sez,

Viruses aren't exactly my area of expertise but let's see if I can point you in the right direction.

First, you need to do some basic flu research. Try googling something like "flu virus biology" for a start.

1. Check out the picture of the flu on ... virus.html
When different viruses are referred to by H and N, it means the two proteins that stick off the flu surface, hemaglutinin and neuroamidase (not sure if I spelled those right!) The flu is always evolving new H and N proteins, that's why it's so hard to design a vaccine--it's a moving target--and why you can get the flu more than once.

2. I think you're on the right track--do some research on how vaccines are produced and how they actually kill it. A big part of what the vaccine scientists do is try to guess what kind of flu will be the big one to worry about in any given year.

3. I googled "immunology" and this was one of the first hits, looks like it might be a nice introduction: ... ology.html

4. I am not sure about this, but your logic makes sense.

5. I found definitions here: ... LView.html
Here is what I THINK they're trying to say--If you get a hit that something matches, it means there were sections of the sequence that matched. Max is the score for the best-matching section, and total is the overall score for all the sections.

You have chosen a really challenging topic, and it's going to take some research to get up to speed. But, it's a very hot topic so I think with some searching you'll find some info on the flu and vaccines. Good luck.

Amber Dance
Science Buddy

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Postby pdoshi » Sat Dec 15, 2007 11:46 am


Here is a detailed website on what are antigens. The website starts of as it beinga immune response in the bodies. There are additional links on this website that might be helpful for your projects. Hope this helps! ... ation.html


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Postby staryl13 » Sat Dec 15, 2007 2:01 pm

Sounds like a really interesting project topic. Here are a couple of links which might help as well- ... 115ft.html ... odies-wap/
Hope this helps, good luck!
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