|
| Taxonomic Classification |
Classifying Your Sequences
Greengenes allows you to submit NAST aligned, non-chimeric FASTA
files to be classified. Greengenes utilizes six
different taxonomies for classifying sequences. Note: Because
Greengenes will classify your sequences with six different taxonomies
you may not find you get a definitive answer as to the specific strain
of bacteria indicated by the submitted sequence. According to one
taxonomy it may be strain X, while for another taxonomy it is reported
as strain Y. You may even find that the same sequence is
classified in completely differing or phyla or classes,
etc, or that one taxonomy classifys it down to the specific strain while another only defines it down to the family level.
To learn more about the taxonomies offered through
Greengenes, click here.
Step 1: Choosing Which Files to Submit to be Classified
Use the "Browse" option to search for the aligned, non-chimeric FASTA file that you would like to have classified.
Step 2: Choosing Significant Match Requirements
For the beginning user, leave both default settings as they are.
- A) The 800 minimum indicates that there must be at
least 800 nucleotide bases to compare in order to consider any
classification match.
- B) The 75% means that this similarity must exist
between the the sequence and the match in the Greengenes library.
Anything less than this will not be considered a match.
Step 3: Delivery Options
Enter the email address to which you
would
like your classification report sent. From Greengenes you will
receive an Excel spreadsheet that has 30 columns. The spreadsheet
is the same five columns of information, just repeated for each of the
six taxonomies used by Greengenes. To see an example of the
spreadsheet you can expect to receive back from Greengenes, along with
an explanation of the five columns of information, click here.
Click here in order to make a tree from your sequences.
Tutorial Main
Greengenes Main
|
|
