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ENSEMBL Special: The Ensembl Web Site: Mechanics of a Genome Browser
- James Stalker,
- Brian Gibbins,
- Patrick Meidl,
- James Smith,
- William Spooner,
- Hans-Rudolf Hotz,
- and Antony V. Cox
Genome Res. May 2004 14: 951-955; doi:10.1101/gr.1863004
...provides similarity searching via BLAST ( Altschul et al. 1990 ) and SSAHA ( Ning et al. 2001 ), rapid retrieval of highly specific data sets with EnsMart ( Kasprzyk et al. 2004 ), and the ability to display and share custom, user-specific data sets via the Distributed Annotation System ( Dowell et al...
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RESOURCE: Exploring relationships and mining data with the UCSC Gene Sorter
- W.J. Kent,
- Fan Hsu,
- Donna Karolchik,
- Robert M. Kuhn,
- Hiram Clawson,
- Heather Trumbower,
- and David Haussler
Genome Res. May 2005 15: 737-741; doi:10.1101/gr.3694705
...., Smedley, D., London, D., Spooner, W., Melsopp, C., Hammond, M., Rocca-Serra, P., Cox, T., and Birney, E. 2004 . EnsMart: A generic system for fast and flexible access to biological data. Genome Res. 14 : 160 –169. ↵ Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A...
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ENSEMBL Special: An Overview of Ensembl
- Ewan Birney,
- T. Daniel Andrews,
- Paul Bevan,
- Mario Caccamo,
- Yuan Chen,
- Laura Clarke,
- Guy Coates,
- James Cuff,
- Val Curwen,
- Tim Cutts,
- Thomas Down,
- Eduardo Eyras,
- Xose M. Fernandez-Suarez,
- Paul Gane,
- Brian Gibbins,
- James Gilbert,
- Martin Hammond,
- Hans-Rudolf Hotz,
- Vivek Iyer,
- Kerstin Jekosch,
- Andreas Kahari,
- Arek Kasprzyk,
- Damian Keefe,
- Stephen Keenan,
- Heikki Lehvaslaiho,
- Graham McVicker,
- Craig Melsopp,
- Patrick Meidl,
- Emmanuel Mongin,
- Roger Pettett,
- Simon Potter,
- Glenn Proctor,
- Mark Rae,
- Steve Searle,
- Guy Slater,
- Damian Smedley,
- James Smith,
- Will Spooner,
- Arne Stabenau,
- James Stalker,
- Roy Storey,
- Abel Ureta-Vidal,
- K. Cara Woodwark,
- Graham Cameron,
- Richard Durbin,
- Anthony Cox,
- Tim Hubbard,
- and Michele Clamp
Genome Res. May 2004 14: 925-928; Published in Advance April 12, 2004, doi:10.1101/gr.1860604
.... Nucleic Acids Res. 32 : 493 -496. ↵ Kasprzyk, A., Keefe, D., Smedley, D., London, D., Spooner, W., Melsopp, C., Hammond, M., Rocca-Serra, P., Cox, T., and Birney, E. 2004 . EnsMart—A generic system for fast and flexible access to biological data. Genome Res. 2004 14 : 160 -169. ↵ Mongin, E., Louis, C...
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ENSEMBL Special: The Ensembl Computing Architecture
- James A. Cuff,
- Guy M.P. Coates,
- Tim J.R. Cutts,
- and Mark Rae
Genome Res. May 2004 14: 971-975; doi:10.1101/gr.1866304
...to compute sequence similarities and execute pattern discovery algorithms to produce gene structures. The data is also denormalized by EnsMart to allow rapid search and queries to take place. The construction of the EnsMart database is a sizable task that requires access to all current Ensembl databases...
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LETTER: Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals
- Ines Hellmann,
- Yuan Mang,
- Zhiping Gu,
- Peter Li,
- Francisco M. de la Vega,
- Andrew G. Clark,
- and Rasmus Nielsen
Genome Res. July 2008 18: 1020-1029; Published in Advance April 14, 2008, doi:10.1101/gr.074187.107
...is the effective population size and μ is the mutation rate per generation. There are several estimators of θ, including the commonly used estimator by Watterson (1975) based on the number of segregating sites. One reason for the interest in this parameter is that it is informative regarding both demographic...
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RESOURCE: WGAViewer: Software for genomic annotation of whole genome association studies
- Dongliang Ge,
- Kunlin Zhang,
- Anna C. Need,
- Olivier Martin,
- Jacques Fellay,
- Thomas J. Urban,
- Amalio Telenti,
- and David B. Goldstein
Genome Res. April 2008 18: 640-643; Published in Advance February 6, 2008, doi:10.1101/gr.071571.107
...of the human . Nature 437 : 1299 – 1320 . ↵ Kasprzyk, A. , Keefe, D. , Smedley, D. , London, D. , Spooner, W. , Melsopp, C. , Hammond, M. , Rocca-Serra, P. , Cox, T. , Birney, E. ( 2004 ) EnsMart: A generic system for fast and flexible access to biological data . Genome Res. 14 : 160 – 169 . ↵ Need, A...
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LETTER: Evolution of alternative splicing after gene duplication
- Zhixi Su,
- Jianmin Wang,
- Jun Yu,
- Xiaoqiu Huang,
- and Xun Gu
Genome Res. February 2006 16: 182-189; Published in Advance December 19, 2005, doi:10.1101/gr.4197006
..., D., Smedley, D., London, D., Spooner, W., Melsopp, C., Hammond, M., Rocca-Serra, P., Cox, T., and Birney, E. 2004 . EnsMart: A generic system for fast and flexible access to biological data. Genome Res. 14 : 160 -169. ↵ Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A...
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ENSEMBL Special: ESTGenes: Alternative Splicing From ESTs in Ensembl
- Eduardo Eyras,
- Mario Caccamo,
- Val Curwen,
- and Michele Clamp
Genome Res. May 2004 14: 976-987; doi:10.1101/gr.1862204
...; the results can be viewed at www.ensembl.org . Each one of the possible transcripts within an ESTGene contains information about the ESTs that were used to build it. ESTGenes are also available in EnsMart ( www.ensembl.org/EnsMart/ ; Kasprzyk et al. 2003 ), in which for the case of human they are also linked...
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ENSEMBL Special: The Ensembl Automatic Gene Annotation System
- Val Curwen,
- Eduardo Eyras,
- T. Daniel Andrews,
- Laura Clarke,
- Emmanuel Mongin,
- Steven M.J. Searle,
- and Michele Clamp
Genome Res. May 2004 14: 942-950; doi:10.1101/gr.1858004
...al. 2003 ). The results of this analysis can be retrieved from EnsMart ( Kasprzyk et al. 2004 ) and will be soon available through the Ensembl Web browser, http://www.ensembl.org . Gene Build Results Ensembl has a large and powerful compute farm, described by Cuff et al. ( 2004 ), and as a result...
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RESOURCE: WormBase as an Integrated Platform for the C. elegans ORFeome
- Nansheng Chen,
- Daniel Lawson,
- Keith Bradnam,
- Todd W. Harris,
- and Lincoln D. Stein
Genome Res. October 15, 2004 14: 2155-2161; doi:10.1101/gr.2521304
...., and Birney, E. 2004 . EnsMart: a generic system for fast and flexible access to biological data. Genome Res. 14 : 160 -169. ↵ Kent, W.J. 2002 . BLAT—the BLAST-like alignment tool. Genome Res. 12 : 656 -664. ↵ Kim, S.K., Lund, J., Kiraly, M., Duke, K., Jiang, M., Stuart, J.M., Eizinger, A., Wylie, B...

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