### A few questions about BLASTing Flu Viruses

Posted:

**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

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

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