NGSEP 4: Efficient and accurate identification of orthogroups and whole‐genome alignment

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 synt...

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Published in:Molecular ecology resources 2023-04, Vol.23 (3), p.712-724
Main Authors: 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
Format: Article
Language:English
Subjects:
Algorithms
Alignment
bioinformatics
comparative genomics
Computer applications
Deoxyribonucleic acid
Developmental biology
DNA
evolution
Gene sequencing
Genome
Genomes
Genomics
Genomics - methods
Graphical user interface
Metagenomics
Nucleotide sequence
Software
Synteny
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Summary: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.
ISSN:1755-098X
1755-0998
DOI:10.1111/1755-0998.13737