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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2021-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0252414 |
| _version_ | 1818834351166586880 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-19T02:33:26Z |
| format | Article |
| id | doaj.art-9cfe9a3bd5f243058243d527c8b69f15 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-19T02:33:26Z |
| publishDate | 2021-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-9cfe9a3bd5f243058243d527c8b69f152022-12-21T20:39:32ZengPublic Library of Science (PLoS)PLoS ONE1932-62032021-01-01165e025241410.1371/journal.pone.0252414PAN2HGENE-tool for comparative analysis and identifying new gene products.Mônica Silva de OliveiraJorianne Thyeska Castro AlvesPablo Henrique Caracciolo Gomes de SáAdonney Allan de Oliveira VerasAdvances 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.https://doi.org/10.1371/journal.pone.0252414 |
| spellingShingle | 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. PLoS ONE |
| title | 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_short | PAN2HGENE-tool for comparative analysis and identifying new gene products. |
| title_sort | pan2hgene tool for comparative analysis and identifying new gene products |
| url | https://doi.org/10.1371/journal.pone.0252414 |
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