FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research.

IF 3.4 4区生物学 Q1 MATHEMATICAL & COMPUTATIONAL BIOLOGY

Database: The Journal of Biological Databases and Curation Pub Date : 2024-06-03 DOI:10.1093/database/baae044

Feng Shao, Minzhi Zeng, Xiaofei Xu, Huahao Zhang, Zuogang Peng

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引用次数: 0

Abstract

We launched the initial version of FishTEDB in 2018, which aimed to establish an open-source, user-friendly, data-rich transposable element (TE) database. Over the past 5 years, FishTEDB 1.0 has gained approximately 10 000 users, accumulating more than 450 000 interactions. With the unveiling of extensive fish genome data and the increasing emphasis on TE research, FishTEDB needs to extend the richness of data and functions. To achieve the above goals, we introduced 33 new fish species to FishTEDB 2.0, encompassing a wide array of fish belonging to 48 orders. To make the updated database more functional, we added a genome browser to visualize the positional relationship between TEs and genes and the estimated TE insertion time in different species. In conclusion, we released a new version of the fish TE database, FishTEDB 2.0, designed to assist researchers in the future study of TE functions and promote the progress of biological theories related to TEs. Database URL: https://www.fishtedb.com/.

查看原文本刊更多论文

FishTEDB 2.0：更新的鱼类转座元件（TE）数据库，具有促进 TE 研究的新功能。

我们于2018年推出了FishTEDB的初始版本，旨在建立一个开源、用户友好、数据丰富的转座元件（TE）数据库。5 年来，FishTEDB 1.0 已拥有约 10 000 名用户，积累了超过 450 000 次交互。随着大量鱼类基因组数据的公布和对转座元件研究的日益重视，FishTEDB 需要扩展丰富的数据和功能。为了实现上述目标，我们在 FishTEDB 2.0 中引入了 33 种新鱼类，涵盖了 48 个目中的各种鱼类。为了使更新后的数据库更具功能性，我们还增加了基因组浏览器，以直观显示 TE 与基因之间的位置关系以及 TE 在不同物种中的估计插入时间。总之，我们发布了新版鱼类 TE 数据库 FishTEDB 2.0，旨在帮助研究人员今后研究 TE 的功能，促进 TE 相关生物学理论的进步。数据库网址：https://www.fishtedb.com/.

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Database: The Journal of Biological Databases and Curation MATHEMATICAL & COMPUTATIONAL BIOLOGY-

CiteScore

9.00

自引率

3.40%

发文量

100

审稿时长

>12 weeks

期刊介绍： Huge volumes of primary data are archived in numerous open-access databases, and with new generation technologies becoming more common in laboratories, large datasets will become even more prevalent. The archiving, curation, analysis and interpretation of all of these data are a challenge. Database development and biocuration are at the forefront of the endeavor to make sense of this mounting deluge of data. Database: The Journal of Biological Databases and Curation provides an open access platform for the presentation of novel ideas in database research and biocuration, and aims to help strengthen the bridge between database developers, curators, and users.