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

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

doi:10.1093/nar/gkab1089

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 journal › Article › peer-review

9 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 language	English (US)
Journal	Nucleic acids research
DOIs	https://doi.org/10.1093/nar/gkab1089
State	Published - 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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1093/nar/gkab1089

https://repository.kaust.edu.sa/bitstream/10754/673931/1/gkab1089.pdf

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@article{906e565e77ec4185806e4ab28caf3fc2,

title = "msRepDB: a comprehensive repetitive sequence database of over 80 000 species.",

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).",

author = "Xingyu Liao and Kang Hu and Adil Salhi and You Zou and Jianxin Wang and Xin Gao",

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",

year = "2021",

month = dec,

day = "1",

doi = "10.1093/nar/gkab1089",

language = "English (US)",

journal = "Nucleic acids research",

issn = "0305-1048",

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T1 - msRepDB: a comprehensive repetitive sequence database of over 80 000 species.

AU - Liao, Xingyu

AU - Hu, Kang

AU - Salhi, Adil

AU - Zou, You

AU - Wang, Jianxin

AU - Gao, Xin

N1 - 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

PY - 2021/12/1

Y1 - 2021/12/1

N2 - 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).

AB - 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).

UR - http://hdl.handle.net/10754/673931

UR - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab1089/6447247

U2 - 10.1093/nar/gkab1089

DO - 10.1093/nar/gkab1089

M3 - Article

C2 - 34850956

SN - 0305-1048

JO - Nucleic acids research

JF - Nucleic acids research

ER -

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

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

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