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.
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for E. coli expression of large protein, insert 6xhis + TEV site using NdeI and BamHI site in pET28a(+), note that it is 6xHis-Thrombin-6xHis-TEV, not continuous 12xHis. BamHI in-frame with tag.
Empty vector for prokaryotic expression, insert a Twin Strep tag (with TAA) between HindII and XhoI site of pET28a (+), both HindIII and XhoI are retained. HindIII in-frame with Twin Strep tag.
Empty vector for prokaryotic expression, insert a Twin Strep tag between NdeI and BamHI site of pET28a (+), both site retained, T7 tag replaced, BamHI site in-frame with Twin Strep tag.
Empty vector for mammalian expression, insert Twin Strep tag using BamHI and AflII site of pcDNA3.1 (-), both site retained, BamHI in-frame with Twin Strep tag
Empty vector for long single strand DNA (up to 1.5k) preparation. This plasmid is a pUC19 with 6 point mutations that remove BspQI, BtsI, BsrDI sites. Mutations adopted from Patent WO/2018/015995.
Empty vector for mammalian expression, insert a Flag tag (with ATG) at XhoI site of pcDNA3.1 (-), xhoI site at 5' of flag tag destroyed, xhoI site at 3' of flag tag retained. XhoI in-frame with Flag
pcDNA3.1 based empty vector for transient transfection of sgRNA-cas9. U6 promoter ~ puro Res cloned from lentiCRISPRv2 (Addgene#52961), lenti virus sequences not included.
Mammalian expression of a EGFP variant. Mutations were adopted from (Addgene#135301, PMC7508230), named msEGFP1.8 because N-ter and C-ter features of that in msGFP2 (PMC7508230) not included.
for in vitro transcription template preparation, insert T7 promoter, TP53 translation initiation site P0 to +670 and F-luc from pGL3-Basic, into pUC19. P0~670 is confusing, BLAST is recommended.