Question: Best method to submit an annotated prokaryotic genome in NCBI
gravatar for Vijay Lakhujani
17 months ago by
Vijay Lakhujani4.0k
Vijay Lakhujani4.0k wrote:

What is the best method to submit prokaryotic genome assemblies along with annotations (mainly the predicted genes, tRNA and rRNA) into NCBI?

I am currently looking at this guideline from NCBI however it is quite confusing. Does someone have a better idea?

Blast2GO also offers preparation of GenBank submission file however it only allows submission of gene (GFF format).

What I have with me is:

  1. Genome assembly in fasta format - pacbio platform , assembled with canu assembler.
  2. Genes predicted by prodigal - gff format and the corresponding proteins/genes in fasta format.
  3. Predicted tRNA, using tRNAScan- locations in bed format.
  4. Predicted rRMA, using RNAmmer- locations in GFF format along with sequences in fasta format.

Any suggestions?

ADD COMMENTlink modified 17 months ago by Juke-342.1k • written 17 months ago by Vijay Lakhujani4.0k
gravatar for Juke-34
17 months ago by
Juke-342.1k wrote:

You could use the beta version of the NCBI gff submission (it looks a bit painful). Or convert your data into EMBL and submit to the european nucleotide archive (ENA) using EMBLmyGFF3 Or convert your data into EMBL and then convert to genebank and then submit to NCBI.

ADD COMMENTlink modified 10 months ago • written 17 months ago by Juke-342.1k

I want the submission in NCBI only. Submission is done by using sequin tool which needs .sqn file. What I could find is that there are 3 mandatory files that needs to created when the genome is required to be submitted along with the annotations using sequin.These are

  1. .sbt file - Template file containing a text ASN.1 Submit-block object
  2. .fsa file - Nucleotide sequence data in FASTA format
  3. .tbl file - Feature Table

These 3 files are required by a tool called tbl2asn which outputs the .sqn file which is submitted using sequin.

ADD REPLYlink modified 17 months ago • written 17 months ago by Vijay Lakhujani4.0k
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