Blast a Sequence

How do I blast a SnapGene sequence against an NCBI database?

Blast a DNA or RNA Sequence

Open a DNA or RNA file and in Map view or Sequence view, click Edit → Select All, or manually select the region of the sequence you wish to "Blast" against an NCBI database.

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To compare the selected nucleotide sequence to an NCBI nucleotide database (blastn):

Click Tools → Blast Selected DNA/RNA → Nucleotide Database....

To compare the translation of the selected nucleotide sequence to an NCBI protein database (blastx):

Click Tools → Blast Selected DNA/RNA → Protein Database....

To compare the translation of the selected nucleotide sequence to a translated NCBI nucleotide database (tblastx):

Click Tools → Blast Selected DNA/RNA → Translated Nucleotide Database....

SnapGene will copy the selected sequence (or translation) and open the appropriate Blast submission page in your default web browser.

Note: If your sequence submission is large then SnapGene will notify you, copy the selected sequences to the clipboard, and request you paste the clipboard into "Query Sequence" field on the NCBI Blast web page.

Blast a Protein Sequence

Open a protein file and in Map view or Sequence view, click Edit → Select All, or manually select the region of the sequence you wish to "Blast" against an NCBI database.

To compare the selected protein sequence to an NCBI Protein database (blastp):

Click Tools → Blast Selected Protein → Protein Database....

To compare the selected protein nucleotide sequence to an NCBI translated nucleotide database (tblastn):

Click Tools → Blast Selected Protein → Translated Nucleotide Database....

SnapGene will copy the selected protein sequence and open the appropriate Blast submission page in your default web browser.

Note: If your sequence submission is large then SnapGene will notify you, copy the selected sequences to the clipboard, and request you paste the clipboard into "Query Sequence" field on the NCBI Blast web page.

Run NCBI Blast

In the browser window, adjust the NCBI Blast parameters if required, then click Blast to run the Blast search.

Import an NCBI "Hit" into Geneious

Use the Accession number (1) and/or range (2) to import the sequence into SnapGene, see Import a Sequence from NCBI.