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

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

doi:10.1093/database/baae044

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

Journal article

Open access

Peer reviewed

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

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

Database : the journal of biological databases and curation, Vol.2024, baae044

2024

DOI: https://doi.org/10.1093/database/baae044

PMID: 38829853

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Abstract

Animals

Databases, Genetic

Databases, Nucleic Acid

DNA Transposable Elements - genetics

Fishes - genetics

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/.

Details

Title: FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research
Authors/Creators: Feng Shao - Southwest University
Minzhi Zeng - Southwest University
Xiaofei Xu
Huahao Zhang - Jiujiang University
Zuogang Peng - Southwest University
Publication Details: Database : the journal of biological databases and curation, Vol.2024, baae044
Publisher: Oxford University Press.
Number of pages: 6
Identifiers: 991005796260207891
Murdoch Affiliation: School of Information Technology
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.54 Molecular & Cell Biology - Genetics; 1.54.1122 Transposable Elements
Web Of Science research areas: Mathematical & Computational Biology
ESI research areas: Biology & Biochemistry