Flu Vaccine and BLAST

[lizdankle]

I want to assess the effectiveness of the flu vaccine in a given year based on the actual isolates that were found that year. I would like to use the BLAST program to do this. If I find the sequence of the isolate and enter it into the BLAST program, I get a list of hits with scores. What I want to do is to see how the sequence of the vaccine compares with the scores of the hits of the BLAST program. How can I do this?

[carolinethorn]

You should be able to get the BLAST results is different formats. I can't tell you exactly where to click without knowing which server you used (BLAST can be run at many different facilities such as entrez/NCBI, ensembl, Baylor medical school website etc) and what settings you chose but generally there should be a way to view the alignments of your sequence alongside the closest matches. SOmetimes its just clicking on the score to view that or the sequence name, or other versions you scroll down and they are at the bottom of the page. Then it gives stars or lines or dots between the 2 where there is an exact match and usually a tally at the end that says how many exactly matched nucleotides there were. The scores are based on the exact match as a proportion of the length of the sequence.

If you need detailed help, please tell us exactly where and what you are looking at in your procedure. Ie. which website you are using to run the blast, if you cahnged any settings or used the default ones and what sequences you used.

Best of luck,
Caroline

[lizdankle]

Thanks for your reply - I am using the NCBI Blast program (blastn). First I went to http://www.cdc.gov/flu/weekly/fluactivity.htm and found the 2 most prevalent type a viruses, and the most prevalent type b virus for the last 4 years. Then I went to http://www.flu.lanl.gov/vaccine/ to find the gene sequences (H4) for these viruses - (not all were available). Then, for each year I am studying, I can find the vaccines used that year and the virus strains selected for each vaccine and do the same procedure to find the gene sequences for the strains in the vaccine.

When the virus strains in the vaccine do not match the actual viruses detected for a given year - I want to compare the sequences of those two strains for similarity. I know I can copy the gene sequence for both the vaccine strain and the actual strain detected and then do a BLAST of each separately but how can I compare two specific virus strains for their similarity using the BLAST program. For example, how do I compare the gene sequence of type A/Fujian H3N2 with type A New Caledonia 20/99.

[carolinethorn]

Hi

Yes, BLAST is a good tool for looking through a large database to find matches to a single given sequence. If you want to compare two (or more) sequences that you already have against each other BLAST is not really the right algorithm for the job. A good program to try would be one called CLUSTALW.
If you google CLUSTALW you should come up with some sites that have webservers to run this program for you. I generally use the one at EBI. It has all of the instructions about how to enter the sequences and get the results. Have a go at running it with your sequences and if you have a problem post back with the details and we can help.

Best of luck,
Caroline

[evilmonkeysrkool]

Go to http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi and you should be able to enter 2 different sequences and compare them.

I was wondering if you knew where to find the raw DNA sequences of the viruses and the vaccines because I couldn't find any that matched up.