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Integrating gene annotation with orthology inference at scale

Kirilenko, Bogdan M. (author)
Max Planck Inst Mol Cell Biol & Genet, D-01307 Dresden, Germany.;Max Planck Inst Phys Komplexer Syst, D-01187 Dresden, Germany.;Ctr Syst Biol Dresden, D-01307 Dresden, Germany.;LOEWE Ctr Translat Biodivers Genom, D-60325 Frankfurt, Germany.;Senckenberg Res Inst, D-60325 Frankfurt, Germany.;Goethe Univ Frankfurt, Fac Biosci, D-60438 Frankfurt, Germany.
Munegowda, Chetan (author)
Max Planck Inst Mol Cell Biol & Genet, D-01307 Dresden, Germany.;Max Planck Inst Phys Komplexer Syst, D-01187 Dresden, Germany.;Ctr Syst Biol Dresden, D-01307 Dresden, Germany.;LOEWE Ctr Translat Biodivers Genom, D-60325 Frankfurt, Germany.;Senckenberg Res Inst, D-60325 Frankfurt, Germany.;Goethe Univ Frankfurt, Fac Biosci, D-60438 Frankfurt, Germany.
Osipova, Ekaterina (author)
Max Planck Inst Mol Cell Biol & Genet, D-01307 Dresden, Germany.;Max Planck Inst Phys Komplexer Syst, D-01187 Dresden, Germany.;Ctr Syst Biol Dresden, D-01307 Dresden, Germany.;LOEWE Ctr Translat Biodivers Genom, D-60325 Frankfurt, Germany.;Senckenberg Res Inst, D-60325 Frankfurt, Germany.;Goethe Univ Frankfurt, Fac Biosci, D-60438 Frankfurt, Germany.
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Jebb, David (author)
Max Planck Inst Mol Cell Biol & Genet, D-01307 Dresden, Germany.;Max Planck Inst Phys Komplexer Syst, D-01187 Dresden, Germany.;Ctr Syst Biol Dresden, D-01307 Dresden, Germany.
Sharma, Virag (author)
Max Planck Inst Mol Cell Biol & Genet, D-01307 Dresden, Germany.;Max Planck Inst Phys Komplexer Syst, D-01187 Dresden, Germany.;Ctr Syst Biol Dresden, D-01307 Dresden, Germany.;Univ Limerick, Sch Nat Sci, Dept Chem Sci, Limerick V94 T9PX, Ireland.
Blumer, Moritz (author)
Max Planck Inst Mol Cell Biol & Genet, D-01307 Dresden, Germany.;Max Planck Inst Phys Komplexer Syst, D-01187 Dresden, Germany.;Ctr Syst Biol Dresden, D-01307 Dresden, Germany.
Morales, Ariadna E. (author)
LOEWE Ctr Translat Biodivers Genom, D-60325 Frankfurt, Germany.;Senckenberg Res Inst, D-60325 Frankfurt, Germany.;Goethe Univ Frankfurt, Fac Biosci, D-60438 Frankfurt, Germany.
Ahmed, Alexis-Walid (author)
LOEWE Ctr Translat Biodivers Genom, D-60325 Frankfurt, Germany.;Senckenberg Res Inst, D-60325 Frankfurt, Germany.;Goethe Univ Frankfurt, Fac Biosci, D-60438 Frankfurt, Germany.
Kontopoulos, Dimitrios-Georgios (author)
LOEWE Ctr Translat Biodivers Genom, D-60325 Frankfurt, Germany.;Senckenberg Res Inst, D-60325 Frankfurt, Germany.;Goethe Univ Frankfurt, Fac Biosci, D-60438 Frankfurt, Germany.
Hilgers, Leon (author)
LOEWE Ctr Translat Biodivers Genom, D-60325 Frankfurt, Germany.;Senckenberg Res Inst, D-60325 Frankfurt, Germany.;Goethe Univ Frankfurt, Fac Biosci, D-60438 Frankfurt, Germany.
Lindblad-Toh, Kerstin (author)
Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
Karlsson, Elinor K. (author)
Broad Inst & Harvard, Cambridge, MA 02139 USA.;UMass Chan Med Sch, Program Bioinformat & Integrat Biol, Worcester, MA 01605 USA.;UMass Chan Med Sch, Program Mol Med, Worcester, MA 01605 USA.
Hiller, Michael (author)
Max Planck Inst Mol Cell Biol & Genet, D-01307 Dresden, Germany.;Max Planck Inst Phys Komplexer Syst, D-01187 Dresden, Germany.;Ctr Syst Biol Dresden, D-01307 Dresden, Germany.;LOEWE Ctr Translat Biodivers Genom, D-60325 Frankfurt, Germany.;Senckenberg Res Inst, D-60325 Frankfurt, Germany.;Goethe Univ Frankfurt, Fac Biosci, D-60438 Frankfurt, Germany.
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Max Planck Inst Mol Cell Biol & Genet, D-01307 Dresden, Germany;Max Planck Inst Phys Komplexer Syst, D-01187 Dresden, Germany.;Ctr Syst Biol Dresden, D-01307 Dresden, Germany.;LOEWE Ctr Translat Biodivers Genom, D-60325 Frankfurt, Germany.;Senckenberg Res Inst, D-60325 Frankfurt, Germany.;Goethe Univ Frankfurt, Fac Biosci, D-60438 Frankfurt, Germany. Max Planck Inst Mol Cell Biol & Genet, D-01307 Dresden, Germany.;Max Planck Inst Phys Komplexer Syst, D-01187 Dresden, Germany.;Ctr Syst Biol Dresden, D-01307 Dresden, Germany. (creator_code:org_t)
American Association for the Advancement of Science (AAAS), 2023
2023
English.
In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6643, s. 368-
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  • Journal article (peer-reviewed)
Abstract Subject headings
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  • 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.

Subject headings

NATURVETENSKAP  -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
NATURVETENSKAP  -- Biologi -- Genetik (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Genetics (hsv//eng)

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