Search by Sequence Information

Search by Sequence Terms

Max Results: user-defined upper limit for the number of target sequences returned
Alignment: region of similarity between target and query sequences
E-value: a BLAST statistic representing the significance of an alignment, values close to zero indicate high sequence similarity with low probability of the similarity occurring by chance
Identities: the number of exact nucleotide matches over the alignment, expressed as a fraction and a percentage
Query Coverage: the length of the query sequence that matches the target sequence in the alignment
Bit Score: a BLAST statistic measuring the quality of an alignment, higher values indicate a more significant match
Span: the length of the alignment, including gaps

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.

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Search plasmids by nucleotide sequence

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

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BLAST Algorithm

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Peter Uetz
Stellberger et al
20162: pGBKCg

pGBKCg Notes

Addgene Diagnostic Digest for 20162

This gel depicts the NEB 1kb ladder and separate digestions of plasmid 20162: pGBKCg with the following enzymes: EcoRI-HF and XhoI

Download Attached File

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