Biological Sequence Quality Control and Organization

NIH Pandemic-Era Grants

Pandemic Era Grants

2024

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Principal Investigator: Eric  Nawrocki
Organization: NATIONAL LIBRARY OF MEDICINE
Fiscal Year: 2024
Award: $250,010
Funding agency: National Library of Medicine

We improved our software package VADR
(https://github.com/nawrockie/vadr) for viral sequence analysis over
the past year.  VADR validates and annotates viral genomes and other
sequences based on comparison and alignment to reference models based
on RefSeq sequences. It is currently used in an automated context to
validate incoming GenBank sequence submissions of Norovirus, Dengue
virus, SARS-CoV-2 and metazoan cytochrome C oxidase subunit 1 (COX1)
protein-coding gene sequences. It is also used in a non-automated,
more manual context for reviewing some RSV, influenza and mpox viral
sequences.

In the past year, we have released influenza models (types A, B, C and
D) and had a paper accepted for publication (but not yet published) in
the journal Database. In that paper, we compared VADR performance for
influenza sequences to that of FLAN, the current tool used for
automated influenza sequence submission analysis at GenBank for the
past several years. We released version 1.6 of VADR in November 2023
which included enhancements to improve handling of influenza sequences
including detection of extra unexpected sequence at the ends of input
genome sequences and validation of intron splice sites.

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