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There are several reasons a record may be flagged, including the detection of a contaminated sequence or a misidentified species. Flags serve two purposes: they act as alerts to inform project managers that an issue has been detected in their records, and they prevent a record from being included in the BOLD ID Engine and Taxonomy Browser. In some cases, changing the taxonomy of the sample or re-editing the sequence can resolve the flags. Once the issue has been resolved, project managers can contact support@boldsystems.org to have the flag removed from their record(s).

BIN assignments are based on sequence divergence, and BINs are generated once per month. Not all sequences will receive a BIN assignment. Currently BINs are only assigned to records with COI sequences longer than 500bp that contain less than 1% ambiguous bases.

If the BOLD ID Engine is not returning any identification matches to your sequence, there may be a few factors worth investigating. First, the genetic marker used must be supported by the database. BOLD currently supports COI for animal identifications, matK and rbcL for plant identifications and ITS for fungal identifications. Second, the sequenced region of the gene should match the marker used. For example, the barcode region for COI is located in the 5’ end. Although other gene regions may return results, most of the database is composed of sequences within the barcode region. Finally, you should ensure the length of your sequence is 180bp or longer. Short sequences and/or those containing a large number of ambiguous bases should be run in the full length database only. If the above factors have been examined and no identifications are returned, please contact support@boldsystems.org and our support staff will be happy to assist you further.

BOLD uses neighbour-joining trees which group sequences together by the number of amino acid or nucleotide differences. The arrangement of the specimens in the tree is based on sequence similarities, with the sequences that are most similar placed closer together on the tree, and with the branch length indicating the degree of similarity. The percentage of similarity between sequences can be measured against the legend (usually 2%) where the longer the branch the more disparity between the sequences. It is often expected that specimens of the same species have more similar sequences and cluster closer together than specimens from different species. Unexpected outcomes can reveal interesting findings, which could be associated with biologically relevant patterns, or they can reveal errors such as misidentification or contamination of a sample. For more information on how to build a Taxon ID Tree, and the parameters you can select to tailor your tree, please refer to the BOLD Handbook. (Note: The BOLD Taxon ID Tree does not infer phylogenetic relationships. There may be many ways to interpret a tree, BOLD encourages that you to use your own discretion in making assumptions from the results).

Short sequences may influence the shape of the Taxon ID Tree based on the alignment algorithm selected while building the tree. The BOLD Aligner is amino acid based, so instead of comparing the nucleotides between the sequences, it compares the amino acid translations. Using this alignment algorithm, short sequences are less likely to align correctly with longer sequences. When building Taxon ID Trees containing short sequences (anything shorter than 200bp), it is recommended to use Muscle or Kalign algorithms. Independent of the alignment algorithm selected, whenever short sequences are included in an analysis, the results should be interpreted with caution.

A dataset is a virtual representation of records stored on BOLD. Records from multiple projects can be added to datasets allowing users to access the data while keeping the records in their original projects. Using datasets, records from multiple projects can be concatenated, analyzed, and even published without ever having to be moved from their original projects. For example, if you are performing a three-year biodiversity study, you may wish to store the records on BOLD in projects based on the year they were collected. If you want to look at all of the Hymenoptera collected over the three years, you can add the appropriate records to a dataset. The records will stay organized in their year-based projects but you can access them all at once and even publish them to GenBank from the dataset. To simplify the publication process, you may also request a DOI (Digital Object Identifier) from BOLD for public datasets. The DOI can be incorporated into the publication so readers will have quick and easy access to the data.

Records submitted through BOLD to GenBank will remain private on GenBank for one year to allow time for submitters to publish their findings before the records are publicly accessible. BOLD recommends all users submit their sequences to GenBank while preparing their manuscript for publication. Once the manuscript is published, users are encouraged to make their data publicly available in BOLD. This can be accomplished by visiting the Modify Project Properties page in the Project Console.

BOLD regularly submits record updates to GenBank, and GenBank will incorporate these changes on a periodic basis. If an update is required within a specific time period, please contact support@boldsystems.org and our support staff will help facilitate the synchronization of BOLD records with GenBank records.

BOLD Systems serves as a workbench for users to organize, analyze, and publish data, with its design and policies recognizing that specimen identification can be a time-consuming process. Consequently, there is no strict timeline for making records public. However, it is recommended that data generated with public funds be released as early as possible, in alignment with open science principles. Instructions for releasing data can be found in the documentation section.

Making a project or dataset public is a straightforward process and project managers can choose to do so at any time. This can be achieved by clicking on Modify Project Properties from within a project or dataset and clicking on the check box that says “Make this project publicly visible”. See the BOLD Handbook for more information. After clicking on save, your project will be publicly accessible through the workbench and the records will be available on BOLD Public Data Portal after it is updated.

You may request to have your images deleted from BOLD at any time by sending an email with your request to support@boldsystems.org.

No, the trace files must be given a new name. Once a trace file has been uploaded to BOLD, whether it succeeded or failed, another trace file with an identical name cannot be uploaded. However, only a small change is required, such as adding a letter or number to the end of the naming scheme of the trace file.

No, the trace files must be given a new name. Once a trace file has been uploaded to BOLD, whether it succeeded or failed, another trace file with an identical name cannot be uploaded. However, only a small change is required, such as adding a letter or number to the end of the naming scheme of the trace file.