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.
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...efficiently packaged into adeno-associated viruses (AAVs) . Other natural Cas orthologs include Hsp1Cas9 ...Mammalian CRISPR libraries have also been created in AAV backbones for in vivo experiments and in a retroviral...capabilities but are small enough to be packaged in AAV particles. Cas13 fusions have also been used in in...
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Original
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...targeting the AAVS1 locus. Doyon Tagging Plasmid: 3xFLAG-2xSTREP Construct for integrating at the AAVS1 "safe ...cloned directly into this vector and targeted to the AAVS1 genomic safe harbor locus using untagged SpCas9 ...Addgene 41815 or #44719 ) in combination with gRNA_AAVS1-T2 (Addgene #41818) or using an all in one vector...vector from the Doyon lab, eSpCas9(1.1)_No_FLAG_AAVS1_T2 (Addgene #79888) , which expresses an untagged...safe harbor" locus: eSpCas9(1.1)_No_FLAG_AAVS1_T2 Doyon Lab TAP Tagging Protocol 97.2 KB Yamamoto PITCh Tagging...