Work

FishTEDB: a collective database of transposable elements identified in the complete genomes of fish

Year: 2017

Type: article

Abstract: Transposable elements (TEs) are important for host gene regulation and genome evolution. Consensus sequences of TEs can assist investigators in accelerating studies on TE origins, amplification, functions and evolution, as well as comparative analyses and prediction of TEs in different species. In evolution, physiology, ecology and heredity research, fish are important models. However, to date, no comprehensive resource for TE consensus sequences exists for fish. Here, we collected genome-wide data and developed a novel database, FishTEDB, including 27 bony fishes, 1 cartilaginous fish, 1 lamprey and 1 lancelet. De novo, structure-based and homology-based approaches were combined to detect TEs. The database is open-source and user-friendly, and users can browse, search and download all data. FishTEDB also provides GetORF, BLAST and HMMER tools to analyze sequences. Database URL: http://www.fishtedb.org/

Source: Database

DOI: 10.1093/database/bax106

Authors: Feng Shao, Jianrong Wang, Hongen Xu, Zuogang Peng

Institutions: Southwest University, Michigan State University, Technical University of Munich

Language: English

Topic: Chromosomal and Genetic Variations

Subfield: Plant Science

Field: Agricultural and Biological Sciences

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $2,729

Funders: Michigan State University, National Natural Science Foundation of China, College of Engineering, Michigan State University, Fundamental Research Funds for the Central Universities