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 annotation using models based on RefSeq annotation. VADR aligns complete input sequences to their nearest RefSeq sequence and uses that alignment to map the RefSeq annotation onto the input sequences. VADR is used by GenBank to help annotate Norovirus, Dengue virus, SARS-CoV-2 and metazoan cytochrome C oxidase subunit 1 (COX1) protein-coding gene sequences. Most of the work in the past year has focused on the development of models for Respiratory Syncytial Virus (RSV) and influenza virus (types A, B, C, and D). Creation of these models motivated the development enhancements to the VADR software for better handling of RSV and influenza sequences. These enhancements include intron splice site validation, extra unexpected sequence at the ends of input sequences, and the ability for VADR to handle alternative coordinates for features that have a diversity of start and stop codon positions. Some of these features were included in the VADR 1.5 release in September of 2022, and the others will be included in the next release of VADR in the coming months.