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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...transfection in:
15 cm dishes OR
CF5 stacks
Select how many dishes or stacks you plan to transfect:
1 to ...following
μg of each plasmid needed per dish or stack. Calculations are based on using 28 μg of total ...) per 15 cm dish or 2500 μg of plasmids per CF5 stack.
Total ug of each plasmid needed for the whole experiment...
...improve resolution, use a stacking gel on top of the resolving gel. A stacking gel typically has a different...of the proteins in a sample migrate through the stacking gel at the same pace and enter the resolving gel...Figure 2: The western blot dry apparatus includes a stack of filter paper, a copper anode/iblot gel matrix...
...
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...
Many thanks to our guest blogger Sean Stacey!
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ART and...ART-induced viral control found in most HIV-1 patients.
Obstacles for CRISPR HIV-1 therapy
Both of these methods...
...for at least six months.
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...
...a double-membrane transfer with a psi membrane stacked behind the p membrane. If your protein runs through...., & Chen, Y. (2011). Prolonged Incubation and Stacked Film Exposure Improve Sensitivity in Western Blotting...