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Resource: Multiple whole-genome alignments without a reference organism
- Inna Dubchak,
- Alexander Poliakov,
- Andrey Kislyuk,
- and Michael Brudno
Genome Res. April 2009 19: 682-689; Published in Advance January 28, 2009, doi:10.1101/gr.081778.108
.... Automated whole multiple alignment of rat, mouse, and human. Genome Res. 14: 685–692. Couronne, O., Poliakov, A., Bray, N., Ishkhanov, T., Ryaboy, D., Rubin, E., Pachter, L., and Dubchak, I. 2003. Strategies and tools for whole alignments. Genome Res. 13: 73–80. Darling, A.C., Mau, B., Blattner, F...
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METHODS: ARACHNE: A Whole-Genome Shotgun Assembler
- Serafim Batzoglou,
- David B. Jaffe,
- Ken Stanley,
- Jonathan Butler,
- Sante Gnerre,
- Evan Mauceli,
- Bonnie Berger,
- Jill P. Mesirov,
- and Eric S. Lander
Genome Res. January 1, 2002 12: 177-189; doi:10.1101/gr.208902
...ARACHNE: A Whole-Genome Shotgun Assembler Serafim Batzoglou 1 , 2 , 3 , David B. Jaffe 2 , 3 , 4 , Ken Stanley 2 , Jonathan Butler 2 , Sante Gnerre 2 , Evan Mauceli 2 , Bonnie Berger 1 , 5 , Jill P. Mesirov...
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LETTER: Comparing Vertebrate Whole-Genome Shotgun Reads to the Human Genome
- Rui Chen,
- John B. Bouck,
- George M. Weinstock,
- and Richard A. Gibbs
Genome Res. November 1, 2001 11: 1807-1816; doi:10.1101/gr.203601
...for understanding the human genome. Methods for using cross-species whole-genome shotgun sequence (WGS) for genome annotation are described in this paper. About one-half million high-quality rat WGS reads (covering 7.5% of the rat genome) generated at the Baylor College of Medicine Human Genome Sequencing Center...
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Methods: Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
- Benedict Paten,
- Javier Herrero,
- Kathryn Beal,
- Stephen Fitzgerald,
- and Ewan Birney
Genome Res. November 2008 18: 1814-1828; Published in Advance October 10, 2008, doi:10.1101/gr.076554.108
...species: human, chimp, baboon, mouse, rat, dog, cat, cow, and pig. The simulations comprise 50 50 k alignments. The mutational operators considered included point substitutions, CpG effects, insertions, including the action of repetitive elements, and, finally, deletions. Parameters for the simulations...
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Methods: Uncertainty in homology inferences: Assessing and improving genomic sequence alignment
- Gerton Lunter,
- Andrea Rocco,
- Naila Mimouni,
- Andreas Heger,
- Alexandre Caldeira,
- and Jotun Hein
Genome Res. February 2008 18: 298-309; Published in Advance December 11, 2007, doi:10.1101/gr.6725608
..., mouse, rat, and dog, and found that addition of in-group species consistently improved the implied human–mouse alignment (Supplemental Fig. S4). Adding all species resulted in an improvement of the sensitivity for human–mouse homology from 82% to 87.4%, similar to or slightly below the sensitivity...
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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
...of whole-genome shotgun (WGS), expressed sequence tag (EST), and mRNA data as a source for the in silico identification of SNPs in gene-coding regions and have identified a large collection of 33,305 high-quality candidate SNPs. Experimental verification of 471 candidate SNPs using a limited set of rat...
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RESOURCE: The Atlas Genome Assembly System
- Paul Havlak,
- Rui Chen,
- K. James Durbin,
- Amy Egan,
- Yanru Ren,
- Xing-Zhi Song,
- George M. Weinstock,
- and Richard A. Gibbs
Genome Res. April 2004 14: 721-732; doi:10.1101/gr.2264004
...with non-sequence-based methods. Use of BACs allows correction of artifacts due to repeats at each stage of the process. This is aided by ancillary data such as BAC fingerprint, other genomic maps, and syntenic relations with other genomes. Atlas was used to assemble a draft DNA sequence of the rat genome...
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ARTICLE: AAA⁺: A Class of Chaperone-Like ATPases Associated with the Assembly, Operation, and Disassembly of Protein Complexes
- Andrew F. Neuwald,
- L. Aravind,
- John L. Spouge,
- and Eugene V. Koonin
Genome Res. January 1, 1999 9: 27-43; doi:10.1101/gr.9.1.27
..., Cold Spring Harbor, New York 11724 USA; 2National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894 USA Abstract Using a combination of computer methods for iterative database searches and multiple sequence alignment, we show that protein sequences...
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LETTER: Identification of Evolutionary Hotspots in the Rodent Genomes
- Von Bing Yap and
- Lior Pachter
Genome Res. April 2004 14: 574-579; doi:10.1101/gr.1967904
...for understanding sequence evolution and for identifying functional elements. We performed a comparative analysis on a whole- multiple alignment of human, mouse, and rat DNA sequences, to describe the average substitution patterns of four types of DNA: ancient repeats, rodent-specific DNA, exons, and conserved...
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Methods: A tale of two templates: Automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices
- Aaron E. Tenney,
- Jia Qian Wu,
- Laura Langton,
- Paul Klueh,
- Ralph Quatrano,
- and Michael R. Brent
Genome Res. February 2007 17: 212-218; Published in Advance January 8, 2007, doi:10.1101/gr.5661407
....F. , Abril, P. , Agarwal, R. , Agarwala, R. , Ainscough, M. , Alexandersson, P. , An, S.E. , et al. ( 2002 ) Initial sequencing and comparative analysis of the mouse . Nature 420 : 520 – 562 . ↵ Wu, J.Q. , Shteynberg, D. , Arumugam, M. , Gibbs, R.A. , Brent, M.R. ( 2004 ) Identification of rat genes...

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