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.
Holiday Schedule: Addgene will be closed December 24th - January 1st. Order processing will resume on January 2, 2026. For questions about estimated ship dates, please feel free to track your order status or contact [email protected].
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...
Second, expansion introduces distortions. The goal in expansion is for your sample to expand evenly in...equipment needed for EM or SRM? Enter Expansion Microscopy.
What is Expansion Microscopy?
ExM provides a straightforward...the protocol, samples can be expanded to ~4-10x linearly! This expansion physically separates molecules...allow for even expansion.
In some cases, labels are added after this stage.
Step 4: Expand! (Typically...are typically easier to expand than mouse brain slices, which are easier to expand than, say, a C. elegans...and after expansion and measure the degree of agreement between them to ensure the expanded images are...lines in pre-expanded samples can sometimes take on a fragmented appearance post-expansion, but that doesn...
...both Addgene’s founding and our growth into the company we are today. As part of our 20th anniversary celebration...with six distributors (Table 1), in China, Korea, Japan, Brazil, India, and Mexico.
Table 2: Addgene distributors...
Summit Pharmaceuticals International
2013
Japan
Leehyo Bioscience
2015
Korea
San Diego...experiments, to enable virtual learning during the pandemic. Feedback like that lets us know that Addgene’...permissions and paperwork. Through updating and expanding our website, we’ve learned about the importance...
...answers uninteresting, the panel members all say the same thing and one panel member dominates the discussion...what is important.
Choose 4 panelists (maybe 5) and no more. Too many panelists will negatively affect timing...will rarely work with a panel if slides are allowed.
Don't put your panelists behind a table. It adds ...Put the panel on a stage if the room is very big, but for an intimate event, put the panelists on the ... the panelists introduce themselves. I do a 1-2 minute introduction. If you chose good panelists, they...nonprofit models that differed from the companies represented on the panel.
This "spontaneous" participation...more great tips on running panel discussions see Guidelines for Great Panels by Scott Kirsner and How to...
...We’re very excited to announce that we are expanding our viral vector service to include a Packaged on... on Request option. Through this expansion, scientists will be able to request an AAV composed of an AAV... vector prep.
Excited? So are we! This expansion will give researchers increased flexibility when...when planning their research and expanded choice when it comes to ordering high-quality materials from...overview in this blog post.
When will the expansion happen?
You will be able to request Packaged ... their material page. Interested scientists can expand the banner to select their serotype of choice, ...through our distributor partners in China, Brazil, Japan, Korea, Mexico, and India. Once the service is launched...
...may be time, then, to look towards genetic code expansion (GCE): techniques in which non-canonical amino...introduced to the bacteria using plasmids. Rapid expansion occurred, with hundreds of new ncAAs and techniques...number of experiments with.
The catch
The rapid expansion of GCE led to the creation of many new tools and...Tan, Z., & Cornish, V. W. (2021). Genetic Code Expansion: A Brief History and Perspective. Biochemistry...
...REC3, and PAM interacting domains and allows for expanded PAM recognition as well as increased specificity...synthetic gRNA) are derived from the same species.
Expanding the CRISPR toolbox
The isolation of novel CRISPR...
... many academic research labs closed during the pandemic, it’s hard to get these reagents. However, when...cell lines, and much more have been critical for pandemic research. Image from Reproducibility for Everyone...additional cell line used in this study came from the Japanese Collection of Research Bioresources Cell Bank,...Biomedical Innovation, Health, and Nutrition in Japan. These results will help researchers choose the... having access to plasmids during the COVID-19 pandemic. Over 7,000 plasmids for COVID-19 research have...strains
Reagents developed during the SARS-CoV pandemic more than a decade ago are now being used to study... continued success of repositories, during the pandemic and in the future, depends on support from the...
...busy in those early years, the founders knew that company culture and enjoying your job were important parts...in between).
Eleven years later, Addgene is a company of fifty instead of three, and we are sending hundreds...Though there still isn't time for goofing off, the company culture here at Addgene has remained paramount....Most Addgenies reply with an enthusiastic, “Our company culture! Addgene is the best place to work, we ...work, we genuinely enjoy each other’s ideas and company.
The Addgene summer picnic
This past weekend was... of University Park at MIT. I’m sure at some companies, employees wouldn’t be caught dead coming into... end, it was another successful event!
Addgene company culture
At Addgene we organically developed the...
...here and now. Our closure was earlier than most companies. Since the start of this crisis, we’ve been very... in our building that someone from a different company had tested positive for COVID-19 (it turned out...viral vector distribution is recovering from the pandemic-related slowdown. More scientists are sharing ...
...build your first panel!
Designing a Panel
In this example, I will describe a basic panel (Table 2, Figure...your "panel". In this blog post, we'll discuss the principles and process of designing a flow panel.
Principles...excitation and emission
Before we design your first panel, we will introduce some background on the color ...laser type. Table adapted from: https://emea.bd.com/panel-design/en/flow-cytometry-fluochrome-brightness-spillover...fluorophore.
Bleeding
Before we start building your first panel, we'll talk about one last principle of color emission...fluorophore-conjugated antibodies together in the same color panel. In this case, make sure to compare the excitation... Hence, they should not be used within the same panel.
Figure 4: Excitation and emission spectra...
...represents the major difference between PACE and PANCE: for PANCE the phage progeny is not diluted out but gets...et al., 2016) and since then has been trying to expand their precision editing capabilities. Base editors...with many Cas domains beyond SpCas9. In order to expand the gene-editing applications and targeting scope...PACE) and Phage-Assisted Non-Continuous Evolution (PANCE) selection systems to engineer better and faster...selection, and replications per day.
The PACE and PANCE systems use M13 bacteriophage, which rely on the...and flexible adenine base editor
Lower-stringency PANCE, followed by higher stringency PACE, resulted in...
... a startup company. However, like many like-minded people, I quickly realize that a company requires more...during graduate school and turn it into a biotech company.
Transitioning an idea from academia to a startup...not remove himself from the idea of starting a company around engineered bacteriophages. He decided to...Development & Operations.
Starting a biotech company
When and how does a startup become "successful...cornerstone of it all. Without a good nucleus, the company won’t go anywhere. The team should initially consist...conversation about its goals and vision for the company; this will help avoid future complications and ...that waste money and time. Most importantly, “the company does not become real until someone takes the risk...
... (Jason Rasgon)
This lab is developing tools for pan-arthropod genetic manipulation. The ReMOT control...scientific sharing
The EDGE Program is designed to expand the number of systems that can be studied by providing...
...Cancer Mutant Collection) or “pan-cancer” analyses across many cancer types (Pan Cancer Mutant Collection)...Cancer Discovery 2016. PubMed PMID: 27147599.
The pan cancer mutant collection and the genetic pathway ...
...gain insight into protein structure and function (Pan et al., 2018).
cDNA libraries, which consist of plasmids...Villalta JE, Chen Y, Whitehead EH, Guimaraes C, Panning B, Ploegh HL, Bassik MC, Qi LS, Kampmann M, Weissman...517:583–588 . https://doi.org/10.1038/nature14136
Pan J, Meyers RM, Michel BC, Mashtalir N, Sizemore AE...
...Kv. C) Cultured rat hippocampal neuron expressing pan-membrane ASAP5. Solid blue circle marks the initiation... soma via the Kv2.1 targeting motif as well as a pan-membrane construct without the Kv motif. Altogether...and the soma. The initiation site identified in panel (C) is indicated; red line is exponential fit. Adapted...
...with Zebrabow
Before the generation of Zebrabow (Pan et al., 2011), Brainbow was also used in zebrafish...Nature 450.7166 (2007): 56. PubMed PMID: 17972876.
Pan, Y. Albert, et al. "Multicolor Brainbow imaging in...cutaneous melanoma induced by mutant BRaf arises from expansion and dedifferentiation of mature pigmented melanocytes...