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Method: Combining DNA and protein alignments to improve genome annotation with LiftOn
- Kuan-Hao Chao,
- Jakob M. Heinz,
- Celine Hoh,
- Alan Mao,
- Alaina Shumate,
- Mihaela Pertea,
- and Steven L. Salzberg
Genome Res. February 2025 35: 311-325; Published in Advance December 27, 2024, doi:10.1101/gr.279620.124
...(NHGRI_mPanTro3-v1.1). (B) Comparative analysis of lifting over annotations from Drosophila melanogaster ( assembly release 6 + ISO1MT) to Drosophila erecta (Prin_Dsim_3.1). (C) Comparative analysis of lifting over annotations from Mus musculus (GRCm39) to Rattus norvegicus (mRatBN7.2). Graphs labeled...
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Letter: A novel active endogenous retrovirus family contributes to genome variability in rat inbred strains
- Yongming Wang,
- František Liška,
- Claudia Gosele,
- Lucie Šedová,
- Vladimír Křen,
- Drahomíra Křenová,
- Zoltán Ivics,
- Norbert Hubner,
- and Zsuzsanna Izsvák
Genome Res. January 2010 20: 19-27; Published in Advance November 3, 2009, doi:10.1101/gr.100073.109
.... In silico searches identified several families that belong to b-ERVs in the rat , including the young, potentially autonomous Rattus norvegicus RnERV-b5 elements (Baillie et al. 2004). Furthermore, in silico sequence analyses predicted two ERV1, as well as four ERV2 families, that may still be active...
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RESOURCE: Single Nucleotide Polymorphisms Associated With Rat Expressed Sequences
- Victor Guryev,
- Eugene Berezikov,
- Rainer Malik,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. July 2004 14: 1438-1443; doi:10.1101/gr.2154304
...-calling quality information not provided by assemblies. Currently, there is only a very limited amount of data available on polymorphisms in the rat ( Rattus norvegicus ), a major model for understanding basic biology and human health and disease. In contrast, there are several thousands of mRNA sequences...
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PERSPECTIVE: Impact of genomics on research in the rat
- Jozef Lazar,
- Carol Moreno,
- Howard J. Jacob,
- and Anne E. Kwitek
Genome Res. December 2005 15: 1717-1728; doi:10.1101/gr.3744005
...Impact of genomics on research in the rat Jozef Lazar , Carol Moreno , Howard J. Jacob , and Anne E. Kwitek 1 Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA Abstract The need to translate genes to function has...
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ARTICLE: Comparative Recombination Rates in the Rat, Mouse, and Human Genomes
- Michael I. Jensen-Seaman,
- Terrence S. Furey,
- Bret A. Payseur,
- Yontao Lu,
- Krishna M. Roskin,
- Chin-Fu Chen,
- Michael A. Thomas,
- David Haussler,
- and Howard J. Jacob
Genome Res. April 2004 14: 528-538; doi:10.1101/gr.1970304
...distantly related species can provide an answer to this question, but to date such estimates of recombination have only been available for invertebrates ( True et al. 1996 ). The recent availability of the complete sequence of the rat ( Rattus norvegicus ; Rat Genome Sequencing Project Consortium [RGSPC...
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LETTER: Genetic Variation in Coding Regions Between and Within Commonly Used Inbred Rat Strains
- Bart M.G. Smits,
- Bert F.M. van Zutphen,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. July 2004 14: 1285-1290; doi:10.1101/gr.2155004
...of mouse inbred strains. Nat. Genet. 24 : 23 –25. ↵ Berezikov, E., Plasterk, R.H., and Cuppen, E. 2002 . GENOTRACE: cDNA-based local GENOme assembly from TRACE archives. Bioinformatics 18 : 1396 –1397. ↵ Canzian, F. 1997 . Phylogenetics of the laboratory rat Rattus norvegicus. Genome Res. 7 : 262 –267...
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LETTER: The Genomic Sequence and Comparative Analysis of the Rat Major Histocompatibility Complex
- Peter Hurt,
- Lutz Walter,
- Ralf Sudbrak,
- Sven Klages,
- Ines Müller,
- Takashi Shiina,
- Hidetoshi Inoko,
- Hans Lehrach,
- Eberhard Günther,
- Richard Reinhardt,
- and Heinz Himmelbauer
Genome Res. April 2004 14: 631-639; doi:10.1101/gr.1987704
...and antigenic basis of tumour transplantation. J. Pathol. Bacteriol. 44 : 691 -697. ↵ Günther, E. and Walter L. 2001 . The major histocompatibility complex of the rat ( Rattus norvegicus ). Immunogenetics 53 : 520 -524. ↵ Hoelsbrekken, S.E., Nylenna, Ø., Saether, P.C., Slettedal, I. Ö., Ryan, J.C., Fossum S...
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LETTER: Genomic Analysis of the Nuclear Receptor Family: New Insights Into Structure, Regulation, and Evolution From the Rat Genome
- Zhengdong Zhang,
- Paula E. Burch,
- Austin J. Cooney,
- Rainer B. Lanz,
- Fred A. Pereira,
- Jiaqian Wu,
- Richard A. Gibbs,
- George Weinstock,
- and David A. Wheeler
Genome Res. April 2004 14: 580-590; doi:10.1101/gr.2160004
...School, Houston, Texas 77225, USA Abstract Completion of the Rattus norvegicus genome sequence enabled a global inventory and analysis of the nuclear receptors (NRs) in three mammalian species. Forty-nine NR members were found in mouse, 48 in human. Forty-seven were found in the rat...
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Method: Chromosome assembly of large and complex genomes using multiple references
- Mikhail Kolmogorov,
- Joel Armstrong,
- Brian J. Raney,
- Ian Streeter,
- Matthew Dunn,
- Fengtang Yang,
- Duncan Odom,
- Paul Flicek,
- Thomas M. Keane,
- David Thybert,
- Benedict Paten,
- and Son Pham
Genome Res. November 2018 28: 1720-1732; Published in Advance October 19, 2018, doi:10.1101/gr.236273.118
...and Rattus norvegicus, we used both of these references for the Ragout 2 assembly. Additionally, for both the M. pahari and M. caroli assemblies, we used the fragments from the other as an extra third reference, as they provided extra adjacencies not observed in the M. musculus and R. norvegicus s. Similar...
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Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
- David Thybert,
- Maša Roller,
- Fábio C.P. Navarro,
- Ian Fiddes,
- Ian Streeter,
- Christine Feig,
- David Martin-Galvez,
- Mikhail Kolmogorov,
- Václav Janoušek,
- Wasiu Akanni,
- Bronwen Aken,
- Sarah Aldridge,
- Varshith Chakrapani,
- William Chow,
- Laura Clarke,
- Carla Cummins,
- Anthony Doran,
- Matthew Dunn,
- Leo Goodstadt,
- Kerstin Howe,
- Matthew Howell,
- Ambre-Aurore Josselin,
- Robert C. Karn,
- Christina M. Laukaitis,
- Lilue Jingtao,
- Fergal Martin,
- Matthieu Muffato,
- Stefanie Nachtweide,
- Michael A. Quail,
- Cristina Sisu,
- Mario Stanke,
- Klara Stefflova,
- Cock Van Oosterhout,
- Frederic Veyrunes,
- Ben Ward,
- Fengtang Yang,
- Golbahar Yazdanifar,
- Amonida Zadissa,
- David J. Adams,
- Alvis Brazma,
- Mark Gerstein,
- Benedict Paten,
- Son Pham,
- Thomas M. Keane,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
...with those of Mus musculus and Rattus norvegicus yields a collection of closely related Muridae s that are similar in phylogenetic structure and divergence times to Hominidae (human–chimp–gorilla–orangutan). This enables direct comparisons of evolutionary dynamics between humans and their most important...
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