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Addgene

Enter a sequence to perform a BLAST-based search of Addgene plasmid sequence databases.

Use Search by Sequence to find plasmids in Addgene's repository containing a specified nucleotide sequence.

About Search by Sequence

  • Search by Sequence performs a nucleotide-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.
    • 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.