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Integrating gene an...
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Kirilenko, Bogdan M.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.
(author)
Integrating gene annotation with orthology inference at scale
- Article/chapterEnglish2023
Publisher, publication year, extent ...
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American Association for the Advancement of Science (AAAS),2023
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printrdacarrier
Numbers
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LIBRIS-ID:oai:DiVA.org:uu-505289
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https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-505289URI
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https://doi.org/10.1126/science.abn3107DOI
Supplementary language notes
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Language:English
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Summary in:English
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
Notes
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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.
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Munegowda, ChetanMax 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.
(author)
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Osipova, EkaterinaMax 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.
(author)
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Jebb, DavidMax 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.
(author)
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Sharma, ViragMax 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.
(author)
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Blumer, MoritzMax 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.
(author)
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Morales, Ariadna E.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.
(author)
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Ahmed, Alexis-WalidLOEWE Ctr Translat Biodivers Genom, D-60325 Frankfurt, Germany.;Senckenberg Res Inst, D-60325 Frankfurt, Germany.;Goethe Univ Frankfurt, Fac Biosci, D-60438 Frankfurt, Germany.
(author)
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Kontopoulos, Dimitrios-GeorgiosLOEWE Ctr Translat Biodivers Genom, D-60325 Frankfurt, Germany.;Senckenberg Res Inst, D-60325 Frankfurt, Germany.;Goethe Univ Frankfurt, Fac Biosci, D-60438 Frankfurt, Germany.
(author)
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Hilgers, LeonLOEWE Ctr Translat Biodivers Genom, D-60325 Frankfurt, Germany.;Senckenberg Res Inst, D-60325 Frankfurt, Germany.;Goethe Univ Frankfurt, Fac Biosci, D-60438 Frankfurt, Germany.
(author)
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Lindblad-Toh, KerstinUppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)kerli865
(author)
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Karlsson, Elinor K.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.
(author)
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Hiller, MichaelMax 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.
(author)
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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)
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In:Science: American Association for the Advancement of Science (AAAS)380:6643, s. 368-+0036-80751095-9203
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