Month: October 2015

Troubleshooting GenBank Submissions: Annotating the Coding Region (CDS)

This article is intended for GenBank data submitters with a basic knowledge of BLAST who submit sequence data from protein-coding genes.

One of the most common problems when submitting DNA or RNA sequence data from protein-coding genes to GenBank is failing to add information about the coding region (often abbreviated as CDS) or incorrectly defining the CDS. Incomplete or incorrect CDS information will prevent you from having accession numbers assigned to your submission data set, but there is a procedure that will help you troubleshoot any problems with the CDS feature annotation: doing a BLAST analysis with your sequences before you submit your data.

NOTE: We have changed BLAST search results displays since publishing this blog. For updated guidance on using Nucleotide BLAST (blastn) to help you troubleshoot coding region annotation, see the articles in the  NCBI Support Center.

Here’s how to use nucleotide BLAST (blastn) and the formatting options menu to analyze, interpret and troubleshoot your submissions:

1. To start the BLAST analysis, go to the BLAST homepage and select “nucleotide blast”.

nucleotide blast link. click to start BLAST analysis
Figure 1. Select “nucleotide blast”.

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