Hello,
I am doing the Blasting Flu Viruses project on this site.
I understand Influenza Viruses and how BLAST works.
I am putting in vaccine strains into blast and getting the values. All of the values are 99% similiar though. Is that right. There are many alignments that are at 99%.
Am I testing the right strains?
What strains to I test against?
Should I just test the most prevalent virus at the time against the vaccine at the time?
What values should I be getting from these tests?
Thanks in advance
PLEASE HELP ASAP
BLASTing Flu Viruses Question PLEASE HELP
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carolinethorn
- Former Expert
- Posts: 393
- Joined: Tue Sep 20, 2005 2:40 pm
Hi,
Thats good that you undestand about viruses and how BLAST works.
One thing that can make a big difference with this project is which database you BLAST your vaccine against and when you run it. This determines how many hits you get. A big database like Genbank at NCBI has millions of sequences, including sequences from organisms and vaccines and many duplicates, so it is quite possible to find many close matches to your vaccine and some of the matches may actually be the same thing just entered into the database by different researchers. So youn eed to look more closely at the description of what the sequence is that it matched to. You may find that several at the top are actually the same. Or it may be that your vaccine is a close match for many influenza strains and other vaccine sequences in the database.
If you want to do a more directed comarison there is a similar type of computer program called CLUSTALW which is for comparing 2 or more known sequences against each other (rather than comparing against a whole database). You could compare theresults you get for comparing your vaccine against the most prevalent strain using this tool.
(If you search the boards you should be able to find other posts I have made about advising people with using CLUSTALW for the Flu vaccine project. )
best of luck,
Caroline
Thats good that you undestand about viruses and how BLAST works.
One thing that can make a big difference with this project is which database you BLAST your vaccine against and when you run it. This determines how many hits you get. A big database like Genbank at NCBI has millions of sequences, including sequences from organisms and vaccines and many duplicates, so it is quite possible to find many close matches to your vaccine and some of the matches may actually be the same thing just entered into the database by different researchers. So youn eed to look more closely at the description of what the sequence is that it matched to. You may find that several at the top are actually the same. Or it may be that your vaccine is a close match for many influenza strains and other vaccine sequences in the database.
If you want to do a more directed comarison there is a similar type of computer program called CLUSTALW which is for comparing 2 or more known sequences against each other (rather than comparing against a whole database). You could compare theresults you get for comparing your vaccine against the most prevalent strain using this tool.
(If you search the boards you should be able to find other posts I have made about advising people with using CLUSTALW for the Flu vaccine project. )
best of luck,
Caroline