PAN2HGENE-tool for comparative analysis and identifying new gene products.

Advances in next-generation sequencing (NGS) platforms have had a positive impact on biological research, leading to the development of numerous omics approaches, including genomics, transcriptomics, metagenomics, and pangenomics. These analyses provide insights into the gene contents of various org...

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Autores principales:	Mônica Silva de Oliveira, Jorianne Thyeska Castro Alves, Pablo Henrique Caracciolo Gomes de Sá, Adonney Allan de Oliveira Veras
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9cfe9a3bd5f243058243d527c8b69f15
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spelling	oai:doaj.org-article:9cfe9a3bd5f243058243d527c8b69f152021-12-02T20:05:25ZPAN2HGENE-tool for comparative analysis and identifying new gene products.1932-620310.1371/journal.pone.0252414https://doaj.org/article/9cfe9a3bd5f243058243d527c8b69f152021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0252414https://doaj.org/toc/1932-6203Advances in next-generation sequencing (NGS) platforms have had a positive impact on biological research, leading to the development of numerous omics approaches, including genomics, transcriptomics, metagenomics, and pangenomics. These analyses provide insights into the gene contents of various organisms. However, to understand the evolutionary processes of these genes, comparative analysis, which is an important tool for annotation, is required. Using comparative analysis, it is possible to infer the functions of gene contents and identify orthologs and paralogous genes via their homology. Although several comparative analysis tools currently exist, most of them are limited to complete genomes. PAN2HGENE, a computational tool that allows identification of gene products missing from the original genome sequence, with automated comparative analysis for both complete and draft genomes, can be used to address this limitation. In this study, PAN2HGENE was used to identify new products, resulting in altering the alpha value behavior in the pangenome without altering the original genomic sequence. Our findings indicate that this tool represents an efficient alternative for comparative analysis, with a simple and intuitive graphical interface. The PAN2HGENE have been uploaded to SourceForge and are available via: https://sourceforge.net/projects/pan2hgene-software.Mônica Silva de OliveiraJorianne Thyeska Castro AlvesPablo Henrique Caracciolo Gomes de SáAdonney Allan de Oliveira VerasPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 5, p e0252414 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mônica Silva de Oliveira Jorianne Thyeska Castro Alves Pablo Henrique Caracciolo Gomes de Sá Adonney Allan de Oliveira Veras PAN2HGENE-tool for comparative analysis and identifying new gene products.
description	Advances in next-generation sequencing (NGS) platforms have had a positive impact on biological research, leading to the development of numerous omics approaches, including genomics, transcriptomics, metagenomics, and pangenomics. These analyses provide insights into the gene contents of various organisms. However, to understand the evolutionary processes of these genes, comparative analysis, which is an important tool for annotation, is required. Using comparative analysis, it is possible to infer the functions of gene contents and identify orthologs and paralogous genes via their homology. Although several comparative analysis tools currently exist, most of them are limited to complete genomes. PAN2HGENE, a computational tool that allows identification of gene products missing from the original genome sequence, with automated comparative analysis for both complete and draft genomes, can be used to address this limitation. In this study, PAN2HGENE was used to identify new products, resulting in altering the alpha value behavior in the pangenome without altering the original genomic sequence. Our findings indicate that this tool represents an efficient alternative for comparative analysis, with a simple and intuitive graphical interface. The PAN2HGENE have been uploaded to SourceForge and are available via: https://sourceforge.net/projects/pan2hgene-software.
format	article
author	Mônica Silva de Oliveira Jorianne Thyeska Castro Alves Pablo Henrique Caracciolo Gomes de Sá Adonney Allan de Oliveira Veras
author_facet	Mônica Silva de Oliveira Jorianne Thyeska Castro Alves Pablo Henrique Caracciolo Gomes de Sá Adonney Allan de Oliveira Veras
author_sort	Mônica Silva de Oliveira
title	PAN2HGENE-tool for comparative analysis and identifying new gene products.
title_short	PAN2HGENE-tool for comparative analysis and identifying new gene products.
title_full	PAN2HGENE-tool for comparative analysis and identifying new gene products.
title_fullStr	PAN2HGENE-tool for comparative analysis and identifying new gene products.
title_full_unstemmed	PAN2HGENE-tool for comparative analysis and identifying new gene products.
title_sort	pan2hgene-tool for comparative analysis and identifying new gene products.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/9cfe9a3bd5f243058243d527c8b69f15
work_keys_str_mv	AT monicasilvadeoliveira pan2hgenetoolforcomparativeanalysisandidentifyingnewgeneproducts AT joriannethyeskacastroalves pan2hgenetoolforcomparativeanalysisandidentifyingnewgeneproducts AT pablohenriquecaracciologomesdesa pan2hgenetoolforcomparativeanalysisandidentifyingnewgeneproducts AT adonneyallandeoliveiraveras pan2hgenetoolforcomparativeanalysisandidentifyingnewgeneproducts
_version_	1718375498745118720

PAN2HGENE-tool for comparative analysis and identifying new gene products.

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