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NGSEP 4: Efficient and accurate identification of orthogroups and whole-genome alignment.
Tello, Daniel; Gonzalez-Garcia, Laura Natalia; Gomez, Jorge; Zuluaga-Monares, Juan Camilo; Garcia, Rogelio; Angel, Ricardo; Mahecha, Daniel; Duarte, Erick; Leon, Maria Del Rosario; Reyes, Fernando; Escobar-Velásquez, Camilo; Linares-Vásquez, Mario; Cardozo, Nicolas; Duitama, Jorge.
Afiliação
  • Tello D; Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
  • Gonzalez-Garcia LN; Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
  • Gomez J; Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
  • Zuluaga-Monares JC; Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
  • Garcia R; Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
  • Angel R; Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
  • Mahecha D; Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
  • Duarte E; Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
  • Leon MDR; Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
  • Reyes F; Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
  • Escobar-Velásquez C; Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
  • Linares-Vásquez M; Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
  • Cardozo N; Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
  • Duitama J; Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
Mol Ecol Resour ; 23(3): 712-724, 2023 Apr.
Article em En | MEDLINE | ID: mdl-36377253
Whole-genome alignment allows researchers to understand the genomic structure and variation among genomes. Approaches based on direct pairwise comparisons of DNA sequences require large computational capacities. As a consequence, pipelines combining tools for orthologous gene identification and synteny have been developed. In this manuscript, we present the latest functionalities implemented in NGSEP 4, to identify orthogroups and perform whole genome alignments. NGSEP implements functionalities for identification of clusters of homologus genes, synteny analysis and whole genome alignment. Our results showed that the NGSEP algorithm for orthogroups identification has competitive accuracy and efficiency in comparison to commonly used tools. The implementation also includes a visualization of the whole genome alignment based on synteny of the orthogroups that were identified, and a reconstruction of the pangenome based on frequencies of the orthogroups among the genomes. NGSEP 4 also includes a new graphical user interface based on the JavaFX technology. We expect that these new developments will be very useful for several studies in evolutionary biology and population genomics.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Software / Genoma Tipo de estudo: Diagnostic_studies Idioma: En Revista: Mol Ecol Resour Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Colômbia País de publicação: Reino Unido
Texto completo
Adicionar na Minha BVS
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Software / Genoma Tipo de estudo: Diagnostic_studies Idioma: En Revista: Mol Ecol Resour Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Colômbia País de publicação: Reino Unido