Addgene Plasmids Track Settings
 
Addgene Plasmid Sequences alignable to the Genome   (All Mapping and Sequencing tracks)

Display mode:   
View table schema
Data last updated: 2020-05-21 21:51:26

Description

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 each plasmid.

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.

Methods

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.

Credits

Thanks to Nathan Mauldin and Jason Fernandes for making this track.

References

References can be found on the specific plasmid's webpage. Each plasmid is hosted by https://www.addgene.org.