Biological Sequence Quality Control and Organization

National Library Of Medicine

Investigators

Linked publications, trials & patents

Abstract

During the past year, we improved our software package VADR (https://github.com/nawrockie/vadr) for viral sequence validation and annotation. VADR is currently used in an automated context to process sequences submissions of Norovirus, dengue virus, SARS-CoV-2 and and metazoan cytochrome C oxidase subunit 1 (COX1) protein-coding gene sequences. It is also used by GenBank sequence curators for reviewing RSV, influenza, and mpox viral sequences. In the past year, GenBank curators we have increased the set of models curators can use by adding parainfluenza virus, human metapneumovirus, herpes simplex virus, measles, mumps, and 229E, NL63, HKU1 and OC43 seasonal coronavirus models through an ongoing collaboration with the Greninger lab at the University of Washington. Additionally, we have developed a new executable program in VADR, called v-scan, which can autodetect the virus species and apply the appropriate set of parameters for that species during annotation. This will allow the software to be more easily applied to other viruses in the future, and allows users to submit sequence files with a mixture of viral sequences in them.