This track shows sequences contained in plasmids that can be ordered through
Addgene. Many plasmids
containing SARS-CoV-2 sequences are now available and more are currently
undergoing quality control analysis. Some of these plasmids are described in
preprints, published articles, and summaries. For a more detailed description
of some of these collections, please see the links to Addgene's webpage for
Some of the following plasmids are available to industry,
in addition to academics and nonprofits. For more information on ordering, the
link to each plasmid's homepage has been provided.
Display Conventions and Configuration
Shown on the genome are regions that can be aligned to a plasmid. The
feature label is the AddGene identifier. A click on a feature shows a
brief description and link to the full webpage for ordering them.
Genbank files were downloaded from Addgene and were parsed to
extract relevant data fields and the plasmid nucleotide sequence. The reference
sequence, SARS-CoV-2 (wuhCor1 - NC_045512v2), was then downloaded from UCSC
browser and a reference database for blast alignment was created using
makeblastdb. The viral region of each plasmid was then aligned using blastn.
Alignments exceeding an expected value of 0.00001 were considered. The aligned
sequences were then converted to bed format and the relevant Genbank data field
were added. Finally, bedToBigBed was used to create the BigBed track.
Thanks to Nathan Mauldin and Jason Fernandes for making this track.
References can be found on the specific plasmid's webpage. Each plasmid is hosted by https://www.addgene.org.