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 or amino acid 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 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.

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Search by SequenceNEW

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Sequence Type

BLAST Database

BLAST Algorithm

Search plasmids by sequence

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

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How do I place an order? Does Addgene accept orders by fax, phone or email?
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How do I get a quote?
What do I need to know about the customs and importation process for my country?
View all Ordering & MTA articles

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Can you help me find a plasmid?
There is a problem with the plasmid I received.
My stab did not grow. What do I do?
What strain of bacteria does my stab contain?
How can I be notified when a new material becomes available?
What services does Addgene provide?
View all Technical Support articles

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How do I prepare and deposit my plasmids?
Which plasmids should I deposit?
How can I track requests for my plasmids?
What are Rewards Points?
View all Depositing Plasmids articles

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What is virus associated DNA, and why do I have to order it?
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Yolanda Schaerli
Santos-Moreno et al
140664: pJ1996_v2

pJ1996_v2 Notes

Addgene Diagnostic Digest

This gel depicts the NEB 1kb ladder and a digestion of the plasmid pJ1996_v2 with the following enzymes: Ncol-HF.

Download Attached File

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