Analyze Sequences on BOLD

BOLD logo

Guide to BOLD for FunDiS Projects [download pdf]

BOLD instructions for changing the name of a specimen [download pdf]

How to use GBIF and NBN Atlas [download pdf]

The FunDis Sequencing Coordinator will email a table of sequence results to Project Leaders that contains the MO or iNat number (Sample ID), the BOLD Processing ID, a consensus ITS barcode sequence with indications of whether it is from a forward, reverse or both reads, and notes if it appears to be a contaminant unrelated to the specimen submitted (or a failed sequence). 

To search for a possible ID in BOLD, you will need to navigate on your browser to http://v4.boldsystems.org/ and register to create a profile, then email the FunDis Sequencing Coordinator requesting access to the data and giving your BOLD username. Log in once you have permission. There are two ways to search for possible matching named species in BOLD.

  1. On the main console page, there is a green menu at the upper right. The second icon is a magnifying glass which takes you to the ID engine. Click this link and then select the 2nd choice: Species Level Barcode Records. This only searches records in the BOLD database, which is very limited for fungi. Copy the ITS sequence (it will be in FASTA file format) and paste it into the box and hit Submit. If it fails to find any matching sequences, it gives a choice to BLAST search in GenBank. Click this link and it will transfer your sequence to the GenBank NCBI search page. Fill in the title blank (e.g., with your specimen number and tentative ID), then hit the blue BLAST button.
  2. Alternatively, when you log in, you will see on the right ‘Recently Accessed’ and a list of project codes to which you have access. Click on the blue code and you will see all of the records in the 96-well plate. At the top it says: ‘Project and dataset search’. Make sure the selection is on ‘code’ and hit the ‘record search’ button. Paste your Process ID’s or your Record IDs (MO or iNat observation number) from the table sent by the Sequencing Coordinator and select the corresponding Identifier code you are searching by, then hit the green Search Records button at the bottom. Hitting the blue Processing code under ‘Sequence Page’ will take you to the ITS consensus sequence and information on the forward and reverse reads. There is a button to download each Trace (chromatogram), but it will take special software such as SnapGene Viewer to be able to open these. For ID search, hit the ‘Identify Sequence’: Full DB button. This search includes all BOLD sequences plus some (but not all) GenBank sequences.

Words of caution

Search engines such as BOLD and GenBank do not necessarily list the best matches at the top. Instead, they weight the match results by the % overlap (coverage) between the sequences, so you will sometimes see high % matches at the top, then declining and then increasing as you go down. Look for % matches of about 97% - 100%, with overlap/coverage of 70% - 100%.

Analysis of BOLD Results

About Fungal Diversity Survey

FunDiS is dedicated to a world in which the fungal kingdom is fully documented, understood, appreciated and protected.

Fungal Diversity Survey
10385 Green Meadow Rd
Sebastopol, CA 95472