If I want to know my sequence I need to compare it to others that are in BoldSystems and Blast. But what is the difference between the two databases? Is one better than the other?
BOLD has only the barcoding fragment, = partial COI sequences (speaking for animals, while other markers for fungi and plants are used), while NCBI has all markers sequenced and published.
In case you have any other sequence than the COI barcoding freagment you must use NCBI Blast (or EMBL, DDBJ).
If you want to identify a species with COI: BOLD has probably the larger set, and it is somehow more reliable (in principle their samples should be curated by specialists, while anyone can send sequences to NCBI). BOLD also includes NCBI entries, while not all BOLD entries are open to the public, therefore are missing in NCBI.
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