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| Alignment: Step 3 |
Step Three in Aligning Your Sequences:
1. There are five options
for returned files. By default the first two options are checked.
Use this default to start. You may also want to check one or more of the other options too.
A. As it says, the first file is an Excel spreadsheet (tab delimited text - not a true spreadsheet) that will tell
you what the outcome is for each of the submitted files. It is
possible that not all of the files you submit will be aligned.
For example, the sequence may be shorter than the default 1250 base length defined in the last step.
B. The second box checked by default is your NAST aligned FASTA
file. You will need this file in order to proceed with checking
for chimeras and ultimately to have your sequences classified.
C.
The third option will return you another FASTA file. This
one will be a collection of the sequences that were not able to be
aligned by NAST.
D. The
fourth and fifth options will add sequences to your NAST aligned FASTA
file. For both options you can choose to have up to five near
neighbor or near neighbor isolates returned for each of your submitted
sequences. This can be a useful tool when classifying your sample
or creating
a tree from your results. To find out more about what near
neighbors and
type strains are and why they are used, click here.
Note: Any duplicates will be removed. If two of your
sequences are taxonomically very close, it would make sense for them to
have similar, if not the same near neighbors or isolates. These
near neighbors or isolates are only added to the FASTA file once, not
once for each and every sequence to which they apply.
2. Click here to move to the next step in alignment.
Near Neighbors
Alignment
Greengenes Main |
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