Review Your BLAST Results

The first step to any sequence analysis is to determine that the sequence being returned matches the specimen it is associated with. This page is not intended to provide a complete discussion on how to make a species determination. It is meant to discuss the first step you should take with any sequence - perform a "sanity check" to ensure that the sequence you have matches the specimen that it should be associated with.

The easiest way to make this determination is through a BLAST search. This search compares the sequences in the public NCBI database called GenBank to the sequence you have received for your specimen. It returns a list of the sequences that are most similar to your specimen. 
 

Step 1 - Review the BLAST page for each of your records by clicking the BLAST "B" on each record.

Clicking this icon will open the results for that record in a new tab. In the center of your dashboard, there will be a large blue "B" next to each record that contains a sequence. Click this "B" and a page showing the closes sequence matches will be displayed in a new tab.

 
On a BLAST page for an individual record, there will be the results from two separate databases. The top set of results are the closest matches from NCBI's GenBank. The bottom set of results are the closest matches from other NAMP projects that are not yet in GenBank.



Step 2 - Ensure your results do not represent a contaminant.

In a small number of cases, the sequence results that come back will represent some kind of contaminant, such as another type of fungi like a yeast or a mold. This is an unavoidable aspect of the process, and is much more common in certain groups, such as jelly fungi. It is also much more common for specimens that were not immediately placed in the dryer or were otherwise dried improperly. If you receive a sequence of a contaminant back, there is little we can do except attempt another DNA extraction from the orignal material. This would be an additional fee and there is no guarantee the next attempt would be successful. Typically, most researchers do not attempt this unless the specimen has some kind of unusual importance.

If you do believe the sequence to be from a contaminant, please complete the following steps:

We do save contaminated sequences in the database. The may serve some type of unusual ecological information in the future. If you believe your seqeunce is a contaminant, we ask that you make the following change to your sequence record:

Clicking the green or red "S" box on your dashboard will open a popup showing the associated sequence record. Under the "Sequences" heading is a link to the record page for your sequence. It is titled "LAC43-MM671" in the image below. Click this link.

On the sequence page, click the "Edit" button to edit your sequence.

In the title bar for the sequence, append "-CONTAMINANT" to the end of the title and hit "Save."

 

Step 3 - Ensure your results consist of the same species the sequence should represent.

Occasionally, specimens become improperly numbered in the field or mixed up in the lab. The final sanity check for sequences is that the genera that most commonly appears in the BLAST results is the same genus that you were expecting the sequence to be. If your BLAST results show the seqeunce represents a Tricholoma, but the specimen is attached to an observation of Polyporus, there is obviously a problem. 

The most typical issue is that two tubes were switched at some point in the process. Once you are done going through your specimens, it is usually possible to find the tube that was switched out. If you are able to find the cause of the error, the simplest fix is to edit the sequence records to be associated with the correct observational report.

If you are unable to find the cause of the error, please alert us to the issue by emailing info@mycoflora.org, and we may be able to find the source of the error.

CLICK HERE for a full primer on how to properly interpret BLAST results for fungi.

About North American Mycoflora Project

We are working towards a single goal - the development of the first comprehensive mycoflora of North America. This project is a consortium of citizen scientists and professional mycologists performing a biological survey of all the macrofungi that occur in North America.

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