Hello,
I have learned that I have to BLAST the influenza viruses and influenza vaccine.
Problems:1) I don't know where to find the influenza viruses sequence
2) How do I compare if they are similar or not? ( Do I compare them myself or does the computer do that for me?)
When I BLAST a sequence there is only one box.
Please write back as soon as possible.
Thank You!
Blasting- Flu viruses and vaccine
Moderators: AmyCowen, kgudger, bfinio, MadelineB, Moderators
Re: Blasting- Flu viruses and vaccine
Hi,
Once you have the name of the virus from the CDC page, you can look the sequences up in the NIH database, here: http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html . I found that it was best to specify the type of flu (A or B), the fact that it was human, segment 4 HA/HE, and then put in the name of the place where the particular virus was isolated into the 'Search by a string' box (the largest one on the right, without a label on top). Searching for years, etc. didn't get me any hits.
There is a modified BLAST program that allows you to compare two sequences, here: http://morag.umsmed.edu/blast/wblast2_cs.html .
Good luck!
Once you have the name of the virus from the CDC page, you can look the sequences up in the NIH database, here: http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html . I found that it was best to specify the type of flu (A or B), the fact that it was human, segment 4 HA/HE, and then put in the name of the place where the particular virus was isolated into the 'Search by a string' box (the largest one on the right, without a label on top). Searching for years, etc. didn't get me any hits.
There is a modified BLAST program that allows you to compare two sequences, here: http://morag.umsmed.edu/blast/wblast2_cs.html .
Good luck!
Re: Blasting- Flu viruses and vaccine
Hello,
I have understood the process of BLASTing flu viruses and vaccines. The only problem is my influenza vaccine and virus are from different years.
For example: I have chosen Southern Hemisphere 2007 vaccine strain A/New Caledonia/20/99 (H1N1)-like virus [HA | NA ], and if I search up New Caledonia for influenza sequence the latest one is from 2004. Does it matter if the vaccine and virus are not from the same year?
My second problem is when blasting the influenza vaccine and virus. Will there be any difference in the results if I paste the vaccine in the first box and the virus in the second/visa versa?
Please write back as soon as possible!
Thank You
I have understood the process of BLASTing flu viruses and vaccines. The only problem is my influenza vaccine and virus are from different years.
For example: I have chosen Southern Hemisphere 2007 vaccine strain A/New Caledonia/20/99 (H1N1)-like virus [HA | NA ], and if I search up New Caledonia for influenza sequence the latest one is from 2004. Does it matter if the vaccine and virus are not from the same year?
My second problem is when blasting the influenza vaccine and virus. Will there be any difference in the results if I paste the vaccine in the first box and the virus in the second/visa versa?
Please write back as soon as possible!
Thank You
Re: Blasting- Flu viruses and vaccine
You don't want the newest one, you want the one specified on the page you found. In this case, you want the specific sequence called A/New Caledonia/20/99 (which was isolated in 1999--hence the 99). However, it looks as if the site you've found it on has the sequence right there--click on the 'HA' button and that should give you the nucleotide sequence of the vaccine.
It does not matter which box you put the vaccine in; the results should be the same either way. However, that's something you could easily test!
It does not matter which box you put the vaccine in; the results should be the same either way. However, that's something you could easily test!