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.