Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2.
Brief Bioinform
; 23(2)2022 03 10.
Artículo
en Inglés
| MEDLINE | ID: covidwho-1639367
ABSTRACT
Genomic epidemiology is important to study the COVID-19 pandemic, and more than two million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic sequences were deposited into public databases. However, the exponential increase of sequences invokes unprecedented bioinformatic challenges. Here, we present the Coronavirus GenBrowser (CGB) based on a highly efficient analysis framework and a node-picking rendering strategy. In total, 1,002,739 high-quality genomic sequences with the transmission-related metadata were analyzed and visualized. The size of the core data file is only 12.20 MB, highly efficient for clean data sharing. Quick visualization modules and rich interactive operations are provided to explore the annotated SARS-CoV-2 evolutionary tree. CGB binary nomenclature is proposed to name each internal lineage. The pre-analyzed data can be filtered out according to the user-defined criteria to explore the transmission of SARS-CoV-2. Different evolutionary analyses can also be easily performed, such as the detection of accelerated evolution and ongoing positive selection. Moreover, the 75 genomic spots conserved in SARS-CoV-2 but non-conserved in other coronaviruses were identified, which may indicate the functional elements specifically important for SARS-CoV-2. The CGB was written in Java and JavaScript. It not only enables users who have no programming skills to analyze millions of genomic sequences, but also offers a panoramic vision of the transmission and evolution of SARS-CoV-2.
Palabras clave
Texto completo:
Disponible
Colección:
Bases de datos internacionales
Base de datos:
MEDLINE
Asunto principal:
Programas Informáticos
/
Vigilancia en Salud Pública
/
Navegador Web
/
SARS-CoV-2
/
COVID-19
Tipo de estudio:
Estudio observacional
Límite:
Humanos
Idioma:
Inglés
Asunto de la revista:
Biologia
/
Informática Médica
Año:
2022
Tipo del documento:
Artículo
País de afiliación:
Bib
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