I've sequenced a 16S rDNA and the result is I only get 599 bp from approximately 1500 bp of the DNA. Is it good or valid to be analyzed by NCBI? I think the long of my 16S rDNA that readable is too short.
I think that it doesn't matter, because when you will blast it, it will be compared to the whole database anyway and you will get your matches. However, it is clear that it is not enough to identify your strain and it will be a partial identification.
Hey, I think just for identification purpose it should be ok but if you want to work on the taxonomy then you need to have around 1400bp 16S rRNA gene sequence. I will recommend EzTaxon (http://www.ezbiocloud.net/eztaxon) for the comparison. NCBI doesn't have any quality criteria for the sequences while in EzTaxon all the sequences are related to type strains only, which makes it better in quality of the sequences.
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