GeneWise and Genomewise
TL;DR: Two algorithms are presented, which predicts gene structure using similar protein sequences, and Genomewise, which provides a gene structure final parse across cDNA- and EST-defined spliced structure.
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Abstract: We present two algorithms in this paper: GeneWise, which predicts gene structure using similar protein sequences, and Genomewise, which provides a gene structure final parse across cDNA- and EST-defined spliced structure. Both algorithms are heavily used by the Ensembl annotation system. The GeneWise algorithm was developed from a principled combination of hidden Markov models (HMMs). Both algorithms are highly accurate and can provide both accurate and complete gene structures when used with the correct evidence.
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Citations
The Rainbow Trout Genome Provides Novel Insights into Evolution after Whole-Genome Duplication in Vertebrates
Yann Guiguen
- 09 Jan 2016
TL;DR: This paper showed that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization.
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Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi
Robert Riley,Asaf Salamov,Daren W. Brown,László Nagy,Dimitrios Floudas,Benjamin W. Held,Anthony Levasseur,Vincent Lombard,Emmanuelle Morin,Robert Otillar,Erika Lindquist,Hui Sun,Kurt LaButti,Jeremy Schmutz,Dina Jabbour,Hong Luo,Scott E. Baker,Antonio G. Pisabarro,Jonathan D. Walton,Robert A. Blanchette,Bernard Henrissat,Francis Martin,Daniel Cullen,David S. Hibbett,Igor V. Grigoriev +24 more
TL;DR: The results indicate that the prevailing paradigm of white rot vs. brown rot does not capture the diversity of fungal wood decay mechanisms, and suggest a continuum rather than a dichotomy between the white-rot and brown-rot modes of wood decay.
GENCODE: producing a reference annotation for ENCODE
Jennifer Harrow,Adam Frankish,Alexandre Reymond,Alexandre Reymond,Chao-Kung Chen,Jacqueline Chrast,Julien Lagarde,James G. R. Gilbert,Roy Storey,David Swarbreck,Colette Rossier,Catherine Ucla,Tim Hubbard,Stylianos E. Antonarakis,Roderic Guigó +14 more
TL;DR: The comprehensiveness of the GENCODE annotation was assessed by attempting to validate all the predicted exon boundaries outside the GencODE annotation, which showed only 40% of GENCode exons are contained within the two sets, which is a reflection of the high number of alternative splice forms with unique exons annotated.
698
Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus.
Jiaming Song,Zhilin Guan,Jianlin Hu,Chaocheng Guo,Zhiquan Yang,Shuo Wang,Dongxu Liu,Bo Wang,Shaoping Lu,Run Zhou,Wen-Zhao Xie,Yuanfang Cheng,Yuting Zhang,Kede Liu,Qingyong Yang,Ling-Ling Chen,Liang Guo +16 more
TL;DR: PAV-based genome-wide association analysis uncovered causal variations for agronomic traits and ecotype differentiation in rapeseed and showed that PAVs in three FLOWERING LOCUS C genes were closely related to flowering time and ecotypes differentiation.
The coffee genome provides insight into the convergent evolution of caffeine biosynthesis
Lorenzo Carretero-Paulet,Alexis Dereeper,Gaëtan Droc,Romain Guyot,Marco Pietrella,Chunfang Zheng,Adriana Alberti,François Anthony,G. Aprea,Jean-Marc Aury,Pascal Bento,Maria Bernard,Stéphanie Bocs,Claudine Campa,Alberto Cenci,Alberto Cenci,Marie Christine Combes,Dominique Crouzillat,Corinne Da Silva,Loretta Daddiego,Fabien De Bellis,Stéphane Dussert,Olivier Garsmeur,Thomas Gayraud,Valentin Guignon,Katharina Jahn,Katharina Jahn,Véronique Jamilloux,Thierry Joët,Karine Labadie,Tianying Lan,Tianying Lan,Julie Leclercq,Maud Lepelley,Thierry Leroy,Leiting Li,Pablo Librado,Loredana Lopez,Adriana Muñoz,Adriana Muñoz,Benjamin Noel,Alberto Pallavicini,Gaetano Perrotta,Valérie Poncet,David Pot,Priyono,Michel Rigoreau,Mathieu Rouard,Julio Rozas,Christine Tranchant-Dubreuil,Robert VanBuren,Qiong Zhang,Alan Carvalho Andrade,Xavier Argout,Benoît Bertrand,Alexandre de Kochko,Giorgio Graziosi,Giorgio Graziosi,Robert J Henry,Jayarama,Ray Ming,Chifumi Nagai,Steve Rounsley,David Sankoff,Giovanni Giuliano,Victor A. Albert,Patrick Wincker,Patrick Wincker,Patrick Wincker,Philippe Lashermes +69 more
TL;DR: The Coffea canephora (coffee) genome was sequenced and identified a conserved gene order, and comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.
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TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
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TL;DR: The results of an international collaboration to produce a high-quality draft sequence of the mouse genome are reported and an initial comparative analysis of the Mouse and human genomes is presented, describing some of the insights that can be gleaned from the two sequences.
Profile hidden Markov models.
TL;DR: Profile HMM methods performed comparably to threading methods in the CASP2 structure prediction exercise and complement standard pairwise comparison methods for large-scale sequence analysis.
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Prediction of Complete Gene Structures in Human Genomic DNA
TL;DR: A general probabilistic model of the gene structure of human genomic sequences which incorporates descriptions of the basic transcriptional, translational and splicing signals, as well as length distributions and compositional features of exons, introns and intergenic regions is introduced.
4.3K
The genome sequence of the filamentous fungus Neurospora crassa
James E. Galagan,Sarah E. Calvo,Katherine A. Borkovich,Eric U. Selker,Nick O. Read,David B. Jaffe,William Fitzhugh,Li-Jun Ma,Serge Smirnov,Seth Purcell,Bushra Rehman,Timothy Elkins,Reinhard Engels,Shunguang Wang,Cydney B. Nielsen,Jonathan Butler,Matthew G. Endrizzi,Dayong Qui,Peter Ianakiev,Deborah Bell-Pedersen,Mary Anne Nelson,Margaret Werner-Washburne,Claude P. Selitrennikoff,John A. Kinsey,Edward L. Braun,Alex Zelter,Alex Zelter,Ulrich Schulte,Gregory O. Kothe,Gregory Jedd,Werner Mewes,Chuck Staben,Edward M. Marcotte,David Greenberg,Alice Roy,Karen Foley,Jerome Naylor,Nicole Stange-Thomann,Robert Barrett,Sante Gnerre,Michael Kamal,Manolis Kamvysselis,Evan Mauceli,Cord Bielke,Stephen Rudd,Dmitrij Frishman,Svetlana Krystofova,Carolyn G. Rasmussen,Robert L. Metzenberg,David D. Perkins,Scott Kroken,Carlo Cogoni,Giuseppe Macino,David E. A. Catcheside,Weixi Li,Robert J. Pratt,Stephen A. Osmani,Colin P.C. DeSouza,Louise Glass,Marc J. Orbach,J. Andrew Berglund,Rodger B. Voelker,Oded Yarden,Michael Plamann,Stephan Seiler,Jay C. Dunlap,Alan Radford,Rodolfo Aramayo,Donald O. Natvig,Lisa A. Alex,Gertrud Mannhaupt,Daniel J. Ebbole,Michael Freitag,Ian T. Paulsen,Matthew S. Sachs,Eric S. Lander,Chad Nusbaum,Bruce W. Birren +77 more
TL;DR: A high-quality draft sequence of the N. crassa genome is reported, suggesting that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.