Hello,
I came across a DNA barcode generation(https://github.com/feldman4/dna-barcodes) according to it the barcode pairs should have minimum distance between them.
from what i understand about this, distance between two barcodes should be great to avoid any chance of similarity due to sequencing error.
Can anyone please correct me?
Yes, it basically means how many operations you need to perform in order to transform one barcode into another. You want a high edit distance so sequencing errors are unlikely to create false-positive barcode matches.
>BC1
ATGGTAGG
>BC2
ATCGTAGG
You obviously do not want two barcodes like this since they differ only by one nucleotide. There are multiple algorithms that define and implement different editing distance such as Hamming and Levenshtein.
Great. But do you know what they mean when they are referring to minimum distance in the above link?
They say guaranteed minimum distance, so I guess (and this would be expected) when you use that tool you get barcodes which differ in, say maybe at least 4 editing steps from each other. You would need to read the docs or source to find out what the guaranteed minimum distance is, but since barcode creation is common these days you are probably good to simply use it at default settings.
Thank a lot. It just clicked me that there is a parameter --distance in the script if the parameter is selected to be 4. They possibly mean, that the barcode distance will be at minimum 4 and can be more than 4 at max. It makes sense now. Thanks again.
Sure, I just accepted it. Thanks for the help.
Log in to answer this question.
Hello Vinay Kusuma!
We believe that this post does not fit the main topic of this site.
SOLVED
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!