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.