Collection location: Richmond, Indiana, USA [Click for map]
Growing at the base of a Pinus nigra.
|User’s votes are weighted by their contribution to the site (log10 contribution). In addition, the user who created the observation gets an extra vote.|
|I’d Call It That||3.0||11.60||2||(Alan Rockefeller,heelsplitter)|
sum(score * weight) /
(total weight + 1)
There are no 100% matches, but there are a whole lot of 99% matches. I think all of the differences between your sequence and the matches in GenBank are due to your sequence being dirty.
A good way to clean up your sequences is to load in the chromatogram into Geneious or the free Snapgene Viewer, and then BLAST your sequence. At each spot that your sequence differs from the closest BLAST match, check the chromatogram. You are using the close BLAST matches as suggested nucleotides in the differing spots.
If your sequence has just one solid peak in that spot, it’s a real difference (or TAQ error). However if you see that the base in the closest BLAST match is present in your read, but at a lower level than other bases, you are usually correct to assume that the reference sequence has the correct base, and you should change your sequence there – especially if that difference is present in several close BLAST matches. I think if you cleaned your sequence in this way you would get several 100% matches with other sequences in GenBank.
Another way to verify the data is to do a reverse read and stitch together the two sequences using Geneious, however this costs extra money is usually not necessary, and in most cases won’t give you better data.
Created: 2015-11-14 03:13:37 CST (-0500)
Last modified: 2018-02-24 01:02:32 CST (-0500)
Viewed: 40 times, last viewed: 2018-05-18 10:53:58 CDT (-0400)