msRepDB: a comprehensive repetitive sequence database of over 80 000 species.

Liao, Xingyu; Hu, Kang; Salhi, Adil; Zou, You; Wang, Jianxin; Gao, Xin

msRepDB: a comprehensive repetitive sequence database of over 80 000 species.

Files

gkab1089.pdf (2.2 MB)

Type

Article

Authors

Liao, Xingyu

Hu, Kang
Salhi, Adil
Zou, You
Wang, Jianxin

Gao, Xin

KAUST Department

Computational Bioscience Research Center (CBRC)
Computer Science Program
Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division
Structural and Functional Bioinformatics Group

KAUST Grant Number

FCC/1/1976-18-01
FCC/1/1976-23-01
FCC/1/1976-25-01
FCC/1/1976-26-01
OSR
REI/1/0018-01-01
REI/1/4216-01-01
REI/1/4437-01-01
REI/1/4473-01-01
REI/1/4742-01
URF/1/4098-01-01
URF/1/4352-01-01
URF/1/4379-01-0

Online Publication Date

2021-12-01

Print Publication Date

2022-01-07

Date

2021-12-01

Abstract

Repeats are prevalent in the genomes of all bacteria, plants and animals, and they cover nearly half of the Human genome, which play indispensable roles in the evolution, inheritance, variation and genomic instability, and serve as substrates for chromosomal rearrangements that include disease-causing deletions, inversions, and translocations. Comprehensive identification, classification and annotation of repeats in genomes can provide accurate and targeted solutions towards understanding and diagnosis of complex diseases, optimization of plant properties and development of new drugs. RepBase and Dfam are two most frequently used repeat databases, but they are not sufficiently complete. Due to the lack of a comprehensive repeat database of multiple species, the current research in this field is far from being satisfactory. LongRepMarker is a new framework developed recently by our group for comprehensive identification of genomic repeats. We here propose msRepDB based on LongRepMarker, which is currently the most comprehensive multi-species repeat database, covering >80 000 species. Comprehensive evaluations show that msRepDB contains more species, and more complete repeats and families than RepBase and Dfam databases. (https://msrepdb.cbrc.kaust.edu.sa/pages/msRepDB/index.html).

Citation

Liao, X., Hu, K., Salhi, A., Zou, Y., Wang, J., & Gao, X. (2021). msRepDB: a comprehensive repetitive sequence database of over 80 000 species. Nucleic Acids Research. doi:10.1093/nar/gkab1089

Acknowledgements

This work was supported by the National Natural Science Foundation of China [62002388,61732009, 61772557, U1909208], King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) [FCC/1/1976-18-01,FCC/1/1976-23-01, FCC/1/1976-25-01, FCC/1/1976-26-01, REI/1/0018-01-01, REI/1/4216-01-01, REI/1/4437-01-01, REI/1/4473-01-01, URF/1/4352-01-01,URF/1/4379-01-01, REI/1/4742-01-01, URF/1/4098-01-01], Hunan Provincial Natural Science Foundation of China [2021JJ40787], Hunan Provincial Science and Technology Program [2018wk4001] and 111 Project [B18059]. This work was carried out in part using computing resources at the High Performance Computing Center of Central South University