stephensons wrote:
Quote:
Just copy and paste the nucleotide sequence into the BLAST search box
http://blast.ncbi.nlm.nih.gov/Blast.cgiSelect "other" database and when you get the result, chose display with "query anchored and dots for match" and new polymorphisms, including A716G will be obvious.
I am doing something wrong, here's what I've done so far:
Basic Blast, then go to Nucleotide Blast, Enter Query Sequence (copy and pasted A/Thessaloniki/225/2010 (H1N1). Run Blast, came up with Graphic Summary/Colour key alignment scores and that's as far as I got. It's a bit confusing.
After the blast there should be a graphic summary and below the graphic summary there are descriptions, and below the descriptions there are alignments.
If you go to the top and click on "formatting options" and unclick "Advanced view" and use the pull down menu for "Alignment View" and select "Query-anchored with dots for identities" and then click on the "Reformat" button, and go down the page, the aligniment view should have the first 60 nucleotides which are labeled "Query". The default is the top 100 matches, so there should be 100 rows which are primarily dots, because each of the top 100 will be isolates that match most of the 60 positions.
If you go down further you will see the next 60 positions. For the above sequence, you won't see a column of letters until you get to the 11th set, which will start with query position 661. Query position 665 has a "G" and the top 8 sequences will have a dot (because they also have a "G"), and most of the next 94 lines will have an "A" (but there are four more which will have a dot). Thus, for position 661 in the query, there are 12 sequences that match A/Thessaloniki/225/2010 including A/Thessaloniki/225/2010 which is at the top of the dot list (query position 665 corresponds to position 715 in HA). The name of the "match" can be seen by clicking on the accession number to the left of the 60 dots. All of those sequences will also have A716G which codes for D225G.
The sequence you chose has A716G as its only change, so if you go to the end of the sequences, you will just see more dots.
Thus, the above sequence has 981 nucleotides, and there is only one difference with the consensus sequence and that difference is A716G, which codes for D225G.
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