CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes

Abstract

Summary While over 200 000 genomic sequences are currently available through dedicated repositories, ad hoc methods for the functional annotation of SARS-CoV-2 genomes do not harness all currently available resources for the annotation of functionally relevant genomic sites. Here, we present CorGAT, a novel tool for the functional annotation of SARS-CoV-2 genomic variants. By comparisons with other state of the art methods we demonstrate that, by providing a more comprehensive and rich annotation, our method can facilitate the identification of evolutionary patterns in the genome of SARS-CoV-2. Availabilityand implementation Galaxy http://corgat.cloud.ba.infn.it/galaxy; software: https://github.com/matteo14c/CorGAT/tree/Revision_V1; docker: https://hub.docker.com/r/laniakeacloud/galaxy_corgat. Supplementary information Supplementary data are available at Bioinformatics online.

A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3′ Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity

“…Similarly, the pangolin pipeline efficiently assigns input viral sequences to SARS-CoV-2 lineages by using sequence alignment and phylogenetic identification and has the potential to infer variants specifically associated to a specific lineage ( Rambaut et al, 2020 ). Also tools such as CorGAT, can assist in the functional annotation of SARS-CoV-2 genomes by sequence alignment and outputting a pseudo-VCF file containing detected variants ( Chiara et al, 2020 ). Clearly, multiple sequence alignment tools are useful in terms of phylogenetic reconstruction and identification, but the process to convert FASTA alignments to variant calls could be ambiguous depending on the variant report format, thus a uniform variant output format such as the Variant Calling Format (VCF) is convenient and suitable for downstream genetic analyses ( Danecek et al, 2011 ).…”

A modular molecular framework for quickly estimating the binding affinity of the spike protein of SARS-CoV-2 variants for ACE2, in presence of mutations at the spike receptor binding domain

“…The rapid spread of new SARS-CoV-2 variants [16,17,50] makes necessary the development of new tools for evaluating the interactions of SARS-CoV-2 proteins for the host cell receptors. A crucial role in SARS-CoV-2 infection is played by the SARS-CoV-2 spike protein, whose interactions with ACE2 receptor triggers pre-/post-fusion conformational changes causing the virus entry into the human cells [1,9].…”

“…Thus, aiming to investigate the effect of amino acid replacement at the SARS-CoV-2 spike RBD, we built a 3D comparative model for each spike variant the spike RBD, namely S477N; E484K). Notably, all the cited VoC genomes have been sequenced in the last year and are responsible for the current pandemics situation [15][16][17][18][19][20][21].…”

Molecular Genetic Analysis of SARS-CoV-2 Lineages in Armenia

“…Variant analysis and functional annotation were performed using the CoVsurver mutation app [23], CoV-GLUE [24], and CorGAT [25] tools. Multiple alignment was performed with the MAFFT version 7 tool.…”