Negligible peptidome diversity of SARS-CoV-2 and its higher taxonomic ranks

Li, Chong; Khan, Mohammad Asif

doi:10.1101/2022.10.31.513750

Cited by 2 publications

(2 citation statements)

References 10 publications

(15 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The tool is publicly available via GitHub (https:// github.com/ ChongLC/ MinimalSetofViralPeptidome-UNIQmin) and PyPI (https:// pypi.org/ project/ uniqmin). The utility of the tool has been demonstrated for the sub-species Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), species Dengue virus and Severe acute respiratory syndrome-related coronavirus, genus Flavivirus and Betacoronavirus, family Flaviviridae and Coronaviridae, and even at the superkingdom rank, all reported viruses (Chong et al, 2021;Chong & Khan, 2022). Herein, we describe a detailed fourpart protocol (Fig.…”

Section: Introductionmentioning

confidence: 99%

A Systematic Bioinformatics Approach for Mapping the Minimal Set of a Viral Peptidome

Chong,

Khan

2024

Current Protocols

View full text Add to dashboard Cite

Sequence changes in viral genomes generate protein sequence diversity that enables viruses to evade the host immune system, hindering the development of effective preventive and therapeutic interventions. The massive proliferation of sequence data provides unprecedented opportunities to study viral adaptation and evolution. An alignment‐free approach removes various restrictions posed by an alignment‐dependent approach for studying sequence diversity. The publicly available tool, UNIQmin, offers an alignment‐free approach for studying viral sequence diversity at any given rank of taxonomy lineage and is big data ready. The tool performs an exhaustive search to determine the minimal set of sequences required to capture the peptidome diversity within a given dataset. This compression is possible through the removal of identical sequences and unique sequences that do not contribute effectively to the peptidome diversity pool. Herein, we describe a detailed four‐part protocol utilizing UNIQmin to generate the minimal set for the purpose of viral diversity analyses, alignment‐free at any rank of the taxonomy lineage, using the recent global public health threat Monkeypox virus (MPX) sequence data as a case study. The protocol enables a systematic bioinformatics approach to study sequence diversity across taxonomic lineages, which is crucial for our future preparedness against viral epidemics. This is particularly important when data are abundant, freely available, and alignment is not an option. © 2024 Wiley Periodicals LLC.Basic Protocol 1: Tool installation and input file preparationBasic Protocol 2: Generation of a minimal set of sequences for a given datasetBasic Protocol 3: Comparative minimal set analysis across taxonomic lineage ranksBasic Protocol 4: Factors affecting the minimal set of sequences

show abstract

Section: Introductionmentioning

confidence: 99%

A Systematic Bioinformatics Approach for Mapping the Minimal Set of a Viral Peptidome

Chong,

Khan

2024

Current Protocols

View full text Add to dashboard Cite

show abstract

“…The tool is publicly available via GitHub (https://github.com/ChongLC/MinimalSetofViralPeptidome-UNIQmin) and PyPI (https://pypi.org/project/uniqmin). The utility of the tool has been demonstrated for the sub-species Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), species Dengue virus and Severe acute respiratory syndrome-related coronavirus , genus Flavivirus and Betacoronavirus , family Flaviviridae and Coronaviridae , and even at the superkingdom rank, all reported Viruses (Chong et al 2021; Chong and Khan 2022). Herein, we focus on describing a detailed three-part protocol (Figure 1) utilizing UNIQmin to address the issue of analysing viral diversity, alignment-free at any rank of the taxonomy lineage, which is much needed in this big data era for our future preparedness of a viral epidemic.…”

Section: Introductionmentioning

confidence: 99%

UNIQmin, an alignment-free tool to study viral sequence diversity across taxonomic lineages: a case study of monkeypox virus

Khan

2022

Preprint

View full text Add to dashboard Cite

Sequence changes in viral genomes generate protein sequence diversity that enable viruses to evade the host immune system, hindering the development of effective preventive and therapeutic interventions. Massive proliferation of sequence data provides unprecedented opportunities to study viral adaptation and evolution. Alignment-free approach removes various restrictions, otherwise posed by an alignment-dependent approach for the study of sequence diversity. The publicly available tool, UNIQmin offers an alignment-free approach for the study of viral sequence diversity at any given rank of taxonomy lineage and is big data ready. The tool performs an exhaustive search to determine the minimal set of sequences required to capture the peptidome diversity within a given dataset. This compression is possible through the removal of identical sequences and unique sequences that do not contribute effectively to the peptidome diversity pool. Herein, we describe a detailed four-part protocol utilizing UNIQmin to generate the minimal set for the purpose of viral diversity analyses at any rank of the taxonomy lineage, using the latest global public health threat monkeypox virus (MPX) as a case study. These protocols enable systematic diversity studies across the taxonomic lineage, which are much needed for our future preparedness of a viral epidemic, in particular when data is in abundance and freely available.

show abstract

Negligible peptidome diversity of SARS-CoV-2 and its higher taxonomic ranks

Cited by 2 publications

References 10 publications

A Systematic Bioinformatics Approach for Mapping the Minimal Set of a Viral Peptidome

A Systematic Bioinformatics Approach for Mapping the Minimal Set of a Viral Peptidome

UNIQmin, an alignment-free tool to study viral sequence diversity across taxonomic lineages: a case study of monkeypox virus

Contact Info

Product

Resources

About