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Print Article: KA-05224

How do I set up Nucleotide BLAST (blastn) to analyze coding regions (CDS) on sequences that I am submitting to GenBank?

You can use a Nucleotide BLAST (blastn) search with the CDS feature display to analyze sequences from protein-coding genes. It will help you determine their properties. At the same time, you can check for any sequencing errors. 

To set up a blastn search:

  • Click the Nucleotide BLAST box on the BLAST home page 
  • Enter your sequence in the Enter Query Sequence box:
    • Paste a single sequence as raw sequence (nucleotides only) or in the FASTA format.
    • For two or more sequences, you must use the FASTA format.
  • Select the Database you want to search. The default selection is Nucleotide collection (nr/nt).
  • Keep the default Program Selection: Highly similar sequences (megablast).  
  • Modify your selection if you don't get any results. You can try alternative programs such as blastx, or genomic blast.
  • Use the BLAST button to run the search.

To set up the CDS feature display on the new BLAST results pages (released in August 2019), follow these steps:  

  • Click the Alignments tab.
  • Use the default, Pairwise, Alignment view. (Or change it based on your preferences.)
  • Click the CDS feature box next to the alignment view selection.

Pairwise alignments from the described search/display consist of several elements. We describe these in the article on interpreting pairwise alignments with CDS feature display.