Detecting putative orthologs.
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The method-reciprocal smallest distance algorithm (rsd)-relies on global sequence alignment and maximum likelihood estimation of evolutionary distances to detect orthologs between two genomes.Abstract:
We developed an algorithm that improves upon the common procedure of taking reciprocal best blast hits(rbh) in the identification of orthologs. The method-reciprocal smallest distance algorithm (rsd)-relies on global sequence alignment and maximum likelihood estimation of evolutionary distances to detect orthologs between two genomes. rsd finds many putative orthologs missed by rbh because it is less likely than rbh to be misled by the presence of a close paralog.read more
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OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
David M. Emms,Steven L. Kelly +1 more
TL;DR: A novel orthogroups inference algorithm called OrthoFinder is provided that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy and utility.
Posted ContentDOI
Protein complex prediction with AlphaFold-Multimer
Richard Evans,Michael J. O'Neill,Alexander Pritzel,Natasha Antropova,Andrew W. Senior,Tim Green,Augustin Žídek,Russell Bates,Sam Blackwell,Jason Yim,Olaf Ronneberger,Sebastian Bodenstein,Michal Zielinski,Alex Bridgland,Anna Potapenko,Andrew Cowie,Kathryn Tunyasuvunakool,R. D. Jain,Ellen Clancy,Pushmeet Kohli,John M. Jumper,Demis Hassabis +21 more
TL;DR: In this article, an AlphaFold model trained specifically for multimeric inputs of known stoichiometry was proposed, which significantly increases the accuracy of predicted multimimeric interfaces over input-adapted single-chain AlphaFolds.
Journal ArticleDOI
Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea
Joelle Amselem,Christina A. Cuomo,Jan A. L. van Kan,Muriel Viaud,Ernesto P. Benito,Arnaud Couloux,Pedro M. Coutinho,Ronald P. de Vries,Paul S. Dyer,Sabine Fillinger,Elisabeth Fournier,Elisabeth Fournier,Lilian Gout,Matthias Hahn,Linda M. Kohn,Nicolas Lapalu,Kim M. Plummer,Jean-Marc Pradier,Emmanuel Quévillon,Emmanuel Quévillon,Amir Sharon,Adeline Simon,Arjen ten Have,Bettina Tudzynski,Paul Tudzynski,Patrick Wincker,Marion Andrew,Véronique Anthouard,Ross E. Beever,Rolland Beffa,Isabelle Benoit,Ourdia Bouzid,Baptiste Brault,Zehua Chen,Mathias Choquer,Mathias Choquer,Jérôme Collemare,Jérôme Collemare,Pascale Cotton,Etienne Danchin,Corinne Da Silva,Angélique Gautier,Corinne Giraud,Tatiana Giraud,Celedonio González,Sandrine Grossetete,Ulrich Güldener,Bernard Henrissat,Barbara J. Howlett,Chinnappa D. Kodira,Matthias Kretschmer,Anne Lappartient,Michaela Leroch,Caroline Levis,Evan Mauceli,Cécile Neuvéglise,Birgitt Oeser,Matthew D. Pearson,Julie Poulain,Nathalie Poussereau,Hadi Quesneville,Christine Rascle,Julia Schumacher,Béatrice Segurens,Adrienne Sexton,Evelyn Silva,Catherine Sirven,Darren M. Soanes,Nicholas J. Talbot,Matthew D. Templeton,Chandri Yandava,Oded Yarden,Qiandong Zeng,Jeffrey A. Rollins,Marc-Henri Lebrun,Marc-Henri Lebrun,Marty Dickman +76 more
TL;DR: Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea, and shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating.
Journal ArticleDOI
Why highly expressed proteins evolve slowly
D. Allan Drummond,Jesse D. Bloom,Christoph Adami,Christoph Adami,Claus O. Wilke,Claus O. Wilke,Frances H. Arnold +6 more
TL;DR: It is hypothesized that selection to reduce the burden of protein misfolding will favor protein sequences with increased robustness to translational missense errors, and genome-wide tests favor the translational robustness explanation over existing hypotheses that invoke constraints on function or translational efficiency.
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Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast.
Adam M. Deutschbauer,Daniel F. Jaramillo,Michael Proctor,Jochen Kumm,Maureen E. Hillenmeyer,Ronald W. Davis,Corey Nislow,Guri Giaever +7 more
TL;DR: The results suggest that the primary mechanism of haploinsufficiency in yeast is due to insufficient protein production, which is alleviated by slowing the growth rate of each strain in minimal media, suggesting that certain genes are rate limiting for growth only in YPD.
References
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Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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Liisa Koski,G. Brian Golding +1 more
TL;DR: The analysis of the genomes of a crenarcheaota species Aeropyrum pernix, an organism with few close relatives fully sequenced, and Escherichia coli, an organisms whose closest relative, Salmonella typhimurium, is completely sequenced are chosen.
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