DynAMic, Université de Lorraine, INRAE, 54000, Nancy, France.
MaIAGE, Université Paris-Saclay, INRAE, 78350, Jouy-en-Josas, France.
BMC Res Notes. 2022 May 10;15(1):157. doi: 10.1186/s13104-022-06036-w.
'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.
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.
“整合子-接合元件”（ICEs）和“整合子-可移动元件”（IMEs）是两类移动遗传元件，其检测和划定较为复杂。因此，它们在细菌基因组中的注释仍不完善。FirmiData 为微生物学家和生物信息学家的科学界提供了一个经注释的 ICEs 和 Firmicutes 中 IMEs 的参考资源。它说明了它们的普遍性和多样性，同时还提供了有关它们组织的信息。FirmiData 的设计目的是通过使用这些 ICEs 和 IMEs 的序列来识别和注释这些元素，从而帮助科学界识别 Firmicutes 中其他基因组中的相关元素。因此，FirmiData 满足了科学界的需求。
FirmiData 提供了在 40 条 Firmicutes 染色体中鉴定出的 98 个 ICEs 和 148 个 IMEs 的手动注释。几乎所有这些元素的核苷酸水平划定都允许对它们携带的基因进行特征描述。
