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About Search by Sequence

Search by Sequence performs a nucleotide-nucleotide or protein-translated nucleotide BLAST search against

Addgene’s plasmid sequence database.

BLAST returns plasmids with similarity to the query sequence.

Results are sorted by E-value, a statistic from BLAST that describes the significance of a match.

Lower values are considered better matches.

FASTA headers and numbers at the beginning of each line will be removed.

The query should only contain DNA characters.

Tips for Success

Enter a distinct sequence that is an important, differentiating feature. For example, the coding region of

a gene, instead of the plasmid origin of replication.

Inspect the percent identity, query coverage, and alignment details to determine if a result match is satisfactory.

Visit the corresponding plasmid webpage to view additional details about a matching plasmid.

If no results are returned:

Try a different isoform or region of the desired sequence.

Choose a different BLAST database. Try the general “All Addgene Plasmids” (default selection),

instead of a specific database, such as “Plant Expression Plasmids”

Try selecting a different BLAST algorithm:

megablast: Designed for comparing sequences within the same, or closely related, species.

Default selection.

blastn: Designed for comparing sequences from different species. May return additional results,

if exact species match is not required.

blastn-short: Optimized for searching with shorter sequences (<= 30 nucleotides)

but can still be effective with slightly larger sequences.

tblastn: Designed for comparing protein sequences against a translated nucleotide sequence database.

Helpful for finding plasmids with codon-optimized sequences.

tblastn-fast: A faster version of tblastn that may return results more quickly, but is less sensitive

There may not be a match in our database.

You can adjust the Max Results setting on the results page from 25 to 500. If many sequences share the same top E-value,

only a truncated set of equally high-scoring matches will be shown. Set the Max Results to 500 to see more matches.

Fill out our Suggest a Plasmid form or

e-mail [email protected] to let us know what we're missing.

By using search by sequence, you understand that some sequences are subject to our Terms of Access and the restrictions contained therein.