The Search By Sequence function allows users to search the Addgene collection based on a specified sequence of interest. This tool performs a nucleotide-nucleotide BLAST search against Addgene’s plasmid sequence database and returns plasmids with similarity to the query sequence.
- Note that Protein BLASTs are not currently available.
To start, select Search By Sequence from the home page or from the search button in the website’s header.
Enter a DNA sequence into the search box. You can enter a FASTA header (>Sequence Name), this header will be removed from the actual search.
Select the portion of the database you want to search (i.e. are you looking for just mammalian expression plasmids or just empty backbones?) and the BLAST algorithm (megablast, blastn, and blastn-short are currently available). And click Search!
- Note that you can find more information on the different BLAST algorithm options as well as additional tips for success by clicking the Information (i) button.
If your search finds any matches, these will be listed below the search box.
- The default number of results shown is 50, but you can adjust the Max Results setting on the results page from 25 to 500.
- For a glossary of Search by Sequence Terms and tips for use, click the Information (i) button below the search box.
Results are primarily sorted by E-value, a statistic from BLAST that describes the significance of a match. Lower values are considered better matches.
Each result card also includes additional information on the alignment(s) to help you determine if a match is suitable. Start by inspecting the percent identity, query coverage, and alignment details.
Some query sequences may have multiple alignments within a plasmid. In this example, we searched for tdTomato which is a tandem dimer. The full query aligns with the tdTomato sequence in this plasmid, but each half of the dimer also aligns partially with the other half – resulting in 3 alignments for this result.
To quickly inspect the plasmid, click the plasmid map to enlarge the image. For full sequence information and more details on a result, visit the corresponding plasmid webpage by clicking the plasmid name.
If your search returns no results, try a different isoform or region of the desired sequence. Some plasmid inserts have been codon-optimized, so may not align well to an expected reference sequence. Additionally, not all sequences in our collection have a full sequence available and partial sequences are easier to miss. For failed sequence searches, it can help to check by using a traditional search as well.
There will be cases where we simply do not have a plasmid that matches your query in our database. If that is the case, feel free to fill out our Suggest a Plasmid form or e-mail help@addgene.org to let us know what we're missing.
Need help with a search or have feedback on this new tool? Email us at help@addgene.org and we will be happy to help.