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Integrating gene annotation with orthology inference at scale. | LitMetric

AI Article Synopsis

  • TOGA (Tool to infer Orthologs from Genome Alignments) unifies the processes of annotating coding genes and inferring orthologs, which have typically been done separately in genomics.
  • This method enhances the detection and annotation of conserved genes, even in fragmented genome assemblies, and can efficiently process hundreds of genomes at once.
  • With its application to 488 placental mammals and 501 bird genomes, TOGA has created expansive comparative gene resources and offers tools for detecting gene losses and assessing genome quality.

Article Abstract

Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10193443PMC
http://dx.doi.org/10.1126/science.abn3107DOI Listing

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