Sequencing Primers - Addgene

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 (