FirmiData: a set of 40 genomes of Firmicutes with a curated annotation of ICEs and IMEs
Abstract Objectives ‘Integrative and Conjugative Elements’ (ICEs) and ‘Integrative and Mobilizable Elements’ (IMEs) are two classes of mobile genetic elements that are complex to detect and delineate. Therefore, they are yet poorly annotated in bacterial genomes. FirmiData provides to the scientific...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-05-01
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| Series: | BMC Research Notes |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13104-022-06036-w |
| _version_ | 1828346960691593216 |
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| author | Gérard Guédon Julie Lao Sophie Payot Thomas Lacroix Hélène Chiapello Nathalie Leblond-Bourget |
| author_facet | Gérard Guédon Julie Lao Sophie Payot Thomas Lacroix Hélène Chiapello Nathalie Leblond-Bourget |
| author_sort | Gérard Guédon |
| collection | DOAJ |
| description | Abstract Objectives ‘Integrative and Conjugative Elements’ (ICEs) and ‘Integrative and Mobilizable Elements’ (IMEs) are two classes of mobile genetic elements that are complex to detect and delineate. Therefore, they are yet poorly annotated in bacterial genomes. FirmiData provides to the scientific community of microbiologists and bioinformaticians a reference resource of annotated ICEs and of IMEs from Firmicutes. It illustrates their prevalence and their diversity but also gives information on their organization. FirmiData was designed to assist the scientific community in identifying and annotating these elements by using the sequences of these ICEs and IMEs for the identification of related elements in other genomes of Firmicutes. Therefore, Firmidata meets the needs of the scientific community. Data description Firmidata provides a manually curated annotation of 98 ICEs and 148 IMEs identified in 40 chromosomes of Firmicutes. The delineation at the nucleotide level of almost all of these elements allows for the characterization of the genes they carry. |
| first_indexed | 2024-04-14T00:33:22Z |
| format | Article |
| id | doaj.art-bb7c1376fea743e7bbdf5e6e5c73587b |
| institution | Directory Open Access Journal |
| issn | 1756-0500 |
| language | English |
| last_indexed | 2024-04-14T00:33:22Z |
| publishDate | 2022-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj.art-bb7c1376fea743e7bbdf5e6e5c73587b2022-12-22T02:22:29ZengBMCBMC Research Notes1756-05002022-05-011511410.1186/s13104-022-06036-wFirmiData: a set of 40 genomes of Firmicutes with a curated annotation of ICEs and IMEsGérard Guédon0Julie Lao1Sophie Payot2Thomas Lacroix3Hélène Chiapello4Nathalie Leblond-Bourget5DynAMic, Université de Lorraine, INRAEDynAMic, Université de Lorraine, INRAEDynAMic, Université de Lorraine, INRAEMaIAGE, Université Paris-Saclay, INRAEMaIAGE, Université Paris-Saclay, INRAEDynAMic, Université de Lorraine, INRAEAbstract Objectives ‘Integrative and Conjugative Elements’ (ICEs) and ‘Integrative and Mobilizable Elements’ (IMEs) are two classes of mobile genetic elements that are complex to detect and delineate. Therefore, they are yet poorly annotated in bacterial genomes. FirmiData provides to the scientific community of microbiologists and bioinformaticians a reference resource of annotated ICEs and of IMEs from Firmicutes. It illustrates their prevalence and their diversity but also gives information on their organization. FirmiData was designed to assist the scientific community in identifying and annotating these elements by using the sequences of these ICEs and IMEs for the identification of related elements in other genomes of Firmicutes. Therefore, Firmidata meets the needs of the scientific community. Data description Firmidata provides a manually curated annotation of 98 ICEs and 148 IMEs identified in 40 chromosomes of Firmicutes. The delineation at the nucleotide level of almost all of these elements allows for the characterization of the genes they carry.https://doi.org/10.1186/s13104-022-06036-wIntegrative and conjugative elementIntegrative and mobilizable elementMobile elementConjugation |
| spellingShingle | Gérard Guédon Julie Lao Sophie Payot Thomas Lacroix Hélène Chiapello Nathalie Leblond-Bourget FirmiData: a set of 40 genomes of Firmicutes with a curated annotation of ICEs and IMEs BMC Research Notes Integrative and conjugative element Integrative and mobilizable element Mobile element Conjugation |
| title | FirmiData: a set of 40 genomes of Firmicutes with a curated annotation of ICEs and IMEs |
| title_full | FirmiData: a set of 40 genomes of Firmicutes with a curated annotation of ICEs and IMEs |
| title_fullStr | FirmiData: a set of 40 genomes of Firmicutes with a curated annotation of ICEs and IMEs |
| title_full_unstemmed | FirmiData: a set of 40 genomes of Firmicutes with a curated annotation of ICEs and IMEs |
| title_short | FirmiData: a set of 40 genomes of Firmicutes with a curated annotation of ICEs and IMEs |
| title_sort | firmidata a set of 40 genomes of firmicutes with a curated annotation of ices and imes |
| topic | Integrative and conjugative element Integrative and mobilizable element Mobile element Conjugation |
| url | https://doi.org/10.1186/s13104-022-06036-w |
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