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

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

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

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).
Original languageEnglish (US)
JournalNucleic acids research
DOIs
StatePublished - Dec 1 2021

Bibliographical note

KAUST Repository Item: Exported on 2021-12-14
Acknowledged KAUST grant number(s): 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
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

ASJC Scopus subject areas

  • Genetics

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