No, “Identify” service can only upload 16S rRNA sequence one by one. And it’s free up to 200 IDs only for academia and non-profit institutions. If you want to upload multi-sequences, we recommend to use commercial ID service, “TrueBac ID-16S” using more stringently validated database. To learn more about TrueBac ID-16S, please visit here.
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EzBioCloud’s 16S database is indeed based on the taxa published on the taxa published in IJSEM. For particular taxa, we assign the representative 16S rRNA sequence based on the TYPE strain. As for individual bacterial isolates, we tend to run quality control by obtaining complete 16S sequence by using multiple rounds of PacBio sequencing. In cases where we see high copy number variants which are also fairly evenly distributed, we usually determine the sample to be contaminated.
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In a single cell of bacteria, the 16S gene copy number can vary as much as up to 15 times among bacterial strains. NGS reads obtained from 16S amplicon samples are assigned to known taxa, and the number of 16S reads can be used to calculate the relative taxonomic abundance. However, to get the true relative taxonomic abundance, the number of 16S reads should be normalized by 16S gene copy number and we finally get the number of cells for each species. EzBioCloud includes 16S gene copy number information for over 3,200 species and the predicted 16S copy number by PICRUSt is provided for the remaining species. To read more about 16S copy number correction, please refer to here.
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We plan to update our database on the quarterly basis.
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Pairwise sequence similarity is the key criterion for microbial identification and as suggested by Kim et al. (2014), a species boundary is defined by a similarity value of 98.65% or greater. In other words, if two sequences show a similarity of 98.65% or less, they belong to different species. BLAST and other services may produce different similarities as they use different algorithms. BLASTN gives identity value which is match/total length, while EzBiocloud gives similarity value which is match/(match+mismatch). We recommend avoiding BLAST for taxonomy-related sequence identity values. To learn more about pairwise nucleotide sequence alignment and how to calculate pairwise sequence similarity, please refer to the links. [Pairwise alignment] [How to calculate similarity]
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Yes, but this function can only be done using the command line tool, OAU. We have an example on our guide here under 'Multiple ANI calculation example'.
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For community users, up to 200 results are saved for 1 year. If 200 IDs were already done and a new result is added, the oldest result will be deleted.
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Yes, EzBioCloud “Identify” engine automatically recognizes reverse-complement sequences. They are corrected before fed to our identification pipeline. We save the corrected sequences in your account, instead of the original version.
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Please watch this video for how to get phylogenetic tree from EzBioCloud “Identify” result. [Watch video]
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