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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...Updated March 6, 2020.
After months of input and polling, Blugene's new virus friend finally has a name!...participation in suggesting names and voting in our poll.
Now, we'd like you to meet.....
*drumroll*
Aavery... out this form here linked below. We’ll keep the poll open until February 28 5PM EST and we’re excited...
...plasmid?
Figure 2: Survey results from a Twitter poll run in 2023, n=194.
After the great Plasmid...much harder to calculate, in both our 2018 and 2023 poll, most people said it took them more than 22 hours...
...advantage of the program.
Start the program by polling the audience with a few questions. Who is out there...in response. I am always ready with some written poll questions to get things started.
Give a couple of...
...relevant parties, and the company at large, by polling and informal communications we made a decision ...scientists often prefer data. At Addgene we rely on polls and surveys. A mix of closed (multiple choice/binary...
...preparation for updating this post, I took an informal poll of Addgene hiring managers. All of them stated that...through in their resumes alone.
In my unofficial poll, hiring managers also said that they considered ...
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...received a research grant in the last five years as polled in the American Association for the Advancement...Transgender issues
Reproductive health
Immigration
Pollution
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Science education
To make scientists...
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Dr. Julio Ernesto Valdivia Silva, Universidad ...related to space medicine.
Now he aims on tracking pollution in rivers by employing synthetic biology resources...
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As biosensors...electrochemical sensors for emerging environmental pollutants.” Front Chem. 2014; 2: 41. PubMed PMID: 25019067...
...guest blogger Pooran Dewari, a postdoc in Steve Pollard’s lab at the MRC Centre for Regenerative Medicine...editing!
Pooran Dewari is a postdoc in Steve Pollard’s lab at the MRC Centre for Regenerative Medicine...