Frequently Asked Questions

Why is it important to add as much biological information about my specimen as possible?

Say you collect a handful of mussels from the beach. You may be fairly confident they are all the same species, they all look the same and there are thousands of them lying around.

However when you barcode your mussels, you find out that instead of one species, you actually have two! And one of them is a new species that no one has discovered before!

You can bet lots of scientists will be very interested in your discovery. They will want to go back to that same beach to collect more samples to study.

As you can imagine, if you did not include your exact collection location on your BOLD-SDP record, no one else will know where to go and your discovery of a new species will likely go unnoticed.

If, on the other hand, you included all the information you can into your record, allowing other scientists to go back to your exact collection site, they will be able to investigate your findings further. Who knows, you might even end up with a new species named after you!

How do I create unique sample IDs?

Sample IDs can be anything you want them to be, as long as they are unique to BOLD. If you are unsure how to create a unique Sample ID try this method:

Year-School Initials-My Initials-Number

For example: 12-JFHS-JS-0001

School Name: John Frasier High School (JFHS)

Student Name: Jane Smith (JS)

It's best to keep your Sample IDs as clear as possible while still containing the information you need. Using a standard Sample ID format for all your samples, like the one shown above, will make it easier to remember it.

If I am unsure about the identification of my specimen, is it better to leave the nomenclature incomplete or to guess?

If you are unsure, leave it blank! You should add as much taxonomic information to your specimen as you can, but only if you're sure it is correct. You can always add more taxonomic information later.

For example, if you know the class of a specimen, but not the order, then leave the order and all the remain taxonomy blank. You can use the Notes field to list any hypotheses you might have about your organism's name.

Once you have a sequence for your specimen, you can use the BOLD ID Engine to determine, or confirm, the identification of your specimen and add it to the record.

What is the difference between region and exact site field in my collection details?

Region refers to a broader area of collection, such as a city, a neighbourhood, or a park, while exact site refers to the exact location where the specimen was found. It is important to make this distinction and fill out your data accordingly, so it is comparable to the data from other students. If you are unsure how specific you should be in describing your exact site, think of it as giving somebody directions to go back to that same spot where you found your sample.

For example: Let's say you found a beautiful beetle in Central Park, New York City. Here is one way to write your collection information:

Region: Central Park, New York City

Exact Site: Shakespeare Park, west of Turtle Pond

This would give a pretty good clue to anyone interested in going back to where you found your beetle.

How do I convert my coordinates into decimal degrees?

BOLD-SDP will only accept GPS coordinates in the decimal degrees format. This is an alternative viewing from the popular degrees, minutes, seconds (DMS) format, but both represent the same location on the map. Many GPS units will have the capability of displaying both formats when recording your coordinates in the field. However there are plenty of free online websites you can use to convert it afterwards too.

Here are a few choices, but feel free to look around and see if you can find one that works for you!

Option 1

Option 2

Option 3

Does the quality of the image I upload to my record really matter?

Yes, it really does! The images associated with your record should be in focus and as close-up as possible, so that all the diagnostic features for your specimen are visible. The images will help you, and other experts, confirm the identifications of your samples, even when the actual specimen is not available.

Comparing a high quality and a low quality image. Notice how the correct image is centered and covers most of image, while the incorrect image takes only 50% of the frame

You can add more than one image per record, so feel free to try all the different orientations – dorsal, ventral, lateral, etc – in case you can’t get all the features you need from just one photo.

What should I do if the species name for my specimen is not on the taxonomy drop down menu?

If the species name for your specimen is not on the drop down menu, it means there are no records on BOLD Systems for that species yet. If this happens, first use the taxonomic databases listed on the Explore Page to see if there are any synonyms for the name you have.

If you cannot find any synonyms for your species, then have your instructor email with the new species name and it will be added to the drop down menu. You may be barcoding a species that is new to the BOLD Systems database!

How do I tell the difference between a good trace and a bad trace?

It is usually pretty easy to tell the difference between a good trace and a bad one. Each of the 4 DNA nucleotides are represented by a specific coloured line, and when the trace quality is high you can decode the sequence of the nucleotides just by looking at the peak of each colored curve one after another. In a bad quality trace file the peaks tend to blend together, so it can be difficult to determine the order of each coloured curve.

The 4 nucleotides are represented by the following colours:

Red = Thymine

Green = Adenine

Black = Guanine

Blue = Cytosine

Good quality trace file

Bad quality trace file. As shown in the image, an N means that the nucleotide is unable to be assigned to one of the 4 nucleotides (unknown colour: yellow).

What are primers and how do I identify them in my sequence?

Primers are short strands of nucleotides used to deliminate the start of DNA synthesis, amplification and/or sequencing. Primers can occur naturally as short RNA strands, but for DNA amplification and sequencing experiments they are usually manufactured in a laboratory. These manufactured primers are typically designed specifically for a group of organisms that share similar DNA sequences, but some primers have the ability to bind to a multitude of organismal groups, and are known as Universal Primers.

In DNA barcoding, where only the mitochondrial COI gene needs to be amplified and sequenced, primers are fundamental because they determine the exact portion of the gene that should be targeted during PCR and sequencing. The sequence codes for the primer are available through the manufacturer, and can be easily recognized in the nucleotide code after DNA sequencing is completed.

It is advisable to trim out the primers before aligning and analyzing your sequences. BOLD-SDP has a built-in sequence processor that will identify and trim your primers automatically. Compare the primer sequences provided by the manufacturer with those identified by BOLD-SDP, chances are they match up very well!