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| Alignment: Step 2 |
Step Two in Aligning Your Sequences:
1. For the 'minimum length' leave it at the
default (1250) unless you know that your sequences are not that large.
If your sequences are too small you will get no returned results
from Greengenes. If you have smaller files you will want to set
the 'minimum length' value below your sequence size. For example,
if your sequences are only 600-900 bases in length, you will want to
set your minimum down at about 500. This will make sure to
include as many sequences as possible. Note: As you lower the minimum you are also, in effect, lowering the accuracy of any matches as less data is being compared.
2.
What Greengene is doing is comparing the sequences that you have
submitted to a database of 16S rRNA genes and looking for a match.
When it finds a match between your sequence and a part of a known
gene in the database it aligns the the two.
3. Click here to move to the next step in alignment..
Alignment
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