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PPanG: a precision pangenome browser enabling nucleotide-level analysis of genomic variations in individual genomes and their graph-based pangenome.
Liu, Mingwei; Zhang, Fan; Lu, Huimin; Xue, Hongzhang; Dong, Xiaorui; Li, Zhikang; Xu, Jianlong; Wang, Wensheng; Wei, Chaochun.
Afiliación
  • Liu M; Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
  • Zhang F; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
  • Lu H; College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
  • Xue H; Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
  • Dong X; Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
  • Li Z; Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
  • Xu J; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
  • Wang W; College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
  • Wei C; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
BMC Genomics ; 25(1): 405, 2024 Apr 24.
Article en En | MEDLINE | ID: mdl-38658835
ABSTRACT
Graph-based pangenome is gaining more popularity than linear pangenome because it stores more comprehensive information of variations. However, traditional linear genome browser has its own advantages, especially the tremendous resources accumulated historically. With the fast-growing number of individual genomes and their annotations available, the demand for a genome browser to visualize genome annotation for many individuals together with a graph-based pangenome is getting higher and higher. Here we report a new pangenome browser PPanG, a precise pangenome browser enabling nucleotide-level comparison of individual genome annotations together with a graph-based pangenome. Nine rice genomes with annotations were provided by default as potential references, and any individual genome can be selected as the reference. Our pangenome browser provides unprecedented insights on genome variations at different levels from base to gene, and reveals how the structures of a gene could differ for individuals. PPanG can be applied to any species with multiple individual genomes available and it is available at https//cgm.sjtu.edu.cn/PPanG .
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Genómica Idioma: En Revista: BMC Genomics Asunto de la revista: GENETICA Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Genómica Idioma: En Revista: BMC Genomics Asunto de la revista: GENETICA Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Reino Unido