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.
The minimum query length is 30 nucleotides. Support for short sequence queries is under development.
Tips for Success
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. 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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Learn more
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Learn more
As part of our Viral Vector Packaging Service, Addgene is distributing ready-to-use viral preparations in engineered systemic serotypes from the Viviana Gradinaru laboratory and the Caltech CLOVER Center (Link opens in a new window). As part of our standard viral production, these viral vectors undergo quality control, including AAV titering by probe-based droplet digital PCR, in vitro and (when possible) in vivo testing, and full sequencing of the final viral vector preparation.
Systemic Delivery AAV Capsid Choice
Need help deciding which capsid to choose? The following decision tree was developed at the CLOVER Center at Caltech and can help guide your decision.
Figure 1: Decision tree for choosing your AAV capsid. Your choice could depend on several factors including: the delivery method, mouse strain, target cell type or tissue of interest, and model organism under study. *Many engineered AAVs for mice use LY6A to cross the blood-brain barrier, leading to strain-specific tropism (See S3 table (Huang, et al., 2019) for LY6A-permissive mouse strains). AAV-PHP.eC, AAV9-X1.1 and AAV1-X1 do not display strain-specific tropism and can be used in LY6A-nonpermissive mouse strains. **AAV1-X1 has not been tested in rats. Abbreviations: AAV, adeno-associated virus; GRE, gene regulatory element; NHP, non-human primate. Image courtesy of the Gradinaru Lab and the Caltech CLOVER Center (Link opens in a new window)and was adapted from Challis et al. (2022). Text version of the AAV decision tree can be found at the bottom of this page.
Our Packaged on Request service offers you even more options. Select from a vast catalog of eligible AAV plasmids and we’ll make the viral vector prep you need.
Or fill out our form to let us know what you would like to see available in viral prep format. Please note this does not guarantee viral vector packaging service, but lets us know what viruses would be helpful to the scientific community.
Text Description for the AAV Decision Tree
The AAV decision tree graphic above helps you choose the best capsid for your cell type. First, do you want to
target CNS or PNS? Then consider species, and then cell type.
