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Research: Venus flytrap carnivorous lifestyle builds on herbivore defense strategies
- Felix Bemm,
- Dirk Becker,
- Christina Larisch,
- Ines Kreuzer,
- Maria Escalante-Perez,
- Waltraud X. Schulze,
- Markus Ankenbrand,
- Anna-Lena Van de Weyer,
- Elzbieta Krol,
- Khaled A. Al-Rasheid,
- Axel Mithöfer,
- Andreas P. Weber,
- Jörg Schultz,
- and Rainer Hedrich
Genome Res. June 2016 26: 812-825; Published in Advance May 4, 2016, doi:10.1101/gr.202200.115
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PERSPECTIVE: Genome annotation past, present, and future: How to define an ORF at each locus
- Michael R. Brent
Genome Res. December 2005 15: 1777-1786; doi:10.1101/gr.3866105
...their true loci from nontranscribed pseudogenes. GeneWise (Birney and Durbin 1997 , 2000 ; Birney et al. 2004b ) is certainly the most important protein-to- alignment program, since it forms a central part of the highly influential Ensembl gene annotation pipeline. The accuracy of GeneWise is determined...
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Research: A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry
- Raghothama Chaerkady,
- Dhanashree S. Kelkar,
- Babylakshmi Muthusamy,
- Kumaran Kandasamy,
- Sutopa B. Dwivedi,
- Nandini A. Sahasrabuddhe,
- Min-Sik Kim,
- Santosh Renuse,
- Sneha M. Pinto,
- Rakesh Sharma,
- Harsh Pawar,
- Nirujogi Raja Sekhar,
- Ajeet Kumar Mohanty,
- Derese Getnet,
- Yi Yang,
- Jun Zhong,
- Aditya P. Dash,
- Robert M. MacCallum,
- Bernard Delanghe,
- Godfree Mlambo,
- Ashwani Kumar,
- T.S. Keshava Prasad,
- Mobolaji Okulate,
- Nirbhay Kumar,
- and Akhilesh Pandey
Genome Res. November 2011 21: 1872-1881; Published in Advance July 27, 2011, doi:10.1101/gr.127951.111
...) discussed the limitations associated with this assembly. A gene set annotated by VectorBase contains both manually annotated genes and predicted gene models from GeneWise (Birney et al. 2004), ClusterMerge (Eyras et al. 2004), and SNAP (Li et al. 2007) algorithms. The VectorBase bioinformatic resource...
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LETTER: Relaxation of yeast mitochondrial functions after whole-genome duplication
- Huifeng Jiang,
- Wenjun Guan,
- David Pinney,
- Wen Wang,
- and Zhenglong Gu
Genome Res. September 2008 18: 1466-1471; Published in Advance July 30, 2008, doi:10.1101/gr.074674.107
....A. ( 2002 ) Planetary biology—Paleontological, geological, and molecular histories of life . Science 296 : 864 – 868 . ↵ Birney, E. , Clamp, M. , Durbin, R. ( 2004 ) GeneWise and Genomewise . Genome Res. 14 : 988 – 995 . ↵ Blank, L.M. , Lehmbeck, F. , Sauer, U. ( 2005 ) Metabolic-flux and network analysis...
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Methods: EGPred: Prediction of Eukaryotic Genes Using Ab Initio Methods After Combining With Sequence Similarity Approaches
- Biju Issac and
- Gajendra Pal Singh Raghava
Genome Res. September 2004 14: 1756-1766; doi:10.1101/gr.2524704
...to identify complete genes ( Guigo et al. 2000 ). A new version of the program, called GenomeWise, uses cDNA and ESTs to define spliced gene structure. GenomeWise and GeneWise are used extensively in the Ensembl annotation pipeline ( Birney et al. 2004 ). Like most alignment methods, these programs...
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LETTER: Evolutionary dynamics of nematode operons: Easy come, slow go
- Wenfeng Qian and
- Jianzhi Zhang
Genome Res. March 2008 18: 412-421; Published in Advance January 24, 2008, doi:10.1101/gr.7112608
...be pseudogenized, equivalent to gene loss. Using GeneWise ( Birney et al. 2004 ), we examined whether the open reading frame (ORF) was still intact for each downstream gene in the broken operons identified above, and found only two cases where the ORFs were disrupted. They are F46B6.6 in C. remanei and F37C12...
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LETTER: Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants
- James H. Thomas
Genome Res. August 2006 16: 1017-1030; Published in Advance July 6, 2006, doi:10.1101/gr.5089806
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Research: The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming
- Sanne Nygaard,
- Guojie Zhang,
- Morten Schiøtt,
- Cai Li,
- Yannick Wurm,
- Haofu Hu,
- Jiajian Zhou,
- Lu Ji,
- Feng Qiu,
- Morten Rasmussen,
- Hailin Pan,
- Frank Hauser,
- Anders Krogh,
- Cornelis J.P. Grimmelikhuijzen,
- Jun Wang,
- and Jacobus J. Boomsma
Genome Res. August 2011 21: 1339-1348; Published in Advance June 30, 2011, doi:10.1101/gr.121392.111
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Resource: Evidence-based gene predictions in plant genomes
- Chengzhi Liang,
- Long Mao,
- Doreen Ware,
- and Lincoln Stein
Genome Res. October 2009 19: 1912-1923; Published in Advance June 18, 2009, doi:10.1101/gr.088997.108
...date are at http:// www..org/cgi/doi/10.1101/gr.088997.108. 1912 Genome Research www..org 19:1912–1923; ISSN 1088-9051/09; www..org Results Data processing pipeline workflow The Gramene gene build is based on the Ensembl pipeline, but with several important modifications. First, while Ensembl uses GeneWise...
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Methods: Genome-wide nucleotide-level mammalian ancestor reconstruction
- Benedict Paten,
- Javier Herrero,
- Stephen Fitzgerald,
- Kathryn Beal,
- Paul Flicek,
- Ian Holmes,
- and Ewan Birney
Genome Res. November 2008 18: 1829-1843; Published in Advance October 10, 2008, doi:10.1101/gr.076521.108
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