Integrating gene annotation with orthology inference at scale
Goethe University Frankfurt · Senckenberg Research Institute and Natural History Museum Frankfurt/M · +7 more institutions
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…
Citation impact
- FWCI
- 28.54
- Percentile
- 100%
- References
- 68
Authors
116- BKBogdan Kirilenko
Goethe University Frankfurt, Senckenberg Research Institute and Natural History Museum Frankfurt/M, Max Planck Institute for the Physics of Complex Systems, LOEWE Centre for Translational Biodiversity Genomics, Center for Systems Biology Dresden, Max Planck Institute of Molecular Cell Biology and Genetics
- CMChetan Munegowda
Goethe University Frankfurt, Senckenberg Research Institute and Natural History Museum Frankfurt/M, Max Planck Institute for the Physics of Complex Systems, LOEWE Centre for Translational Biodiversity Genomics, Center for Systems Biology Dresden, Max Planck Institute of Molecular Cell Biology and Genetics
- EOEkaterina Osipova
Goethe University Frankfurt, Senckenberg Research Institute and Natural History Museum Frankfurt/M, Max Planck Institute for the Physics of Complex Systems, LOEWE Centre for Translational Biodiversity Genomics, Center for Systems Biology Dresden, Max Planck Institute of Molecular Cell Biology and Genetics
- DJDavid Jebb
Max Planck Institute for the Physics of Complex Systems, Center for Systems Biology Dresden, Max Planck Institute of Molecular Cell Biology and Genetics
- VSVirag Sharma
Max Planck Institute for the Physics of Complex Systems, Center for Systems Biology Dresden, Max Planck Institute of Molecular Cell Biology and Genetics
Topics & keywords
- Annotation
- Genome
- Inference
- Biology
- Gene
- Gene Annotation
- Computational biology
- Genomics