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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
...2 : 7 . ↵ Eyras, E., Caccamo, M., Curwen, V., and Clamp, M. 2004 . ESTGenes: Alternative splicing from ESTs in Ensembl. Genome Res. (this issue). ↵ Karolchik, D., Hinrichs, A.S., Furey, T.S., Roskin, K.M., Sugnet, C.W., Haussler, D., and Kent, W.J. 2004 . The UCSC Table Browser data retrieval tool...
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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
...) with parameters set such that the exon boundaries are not modified. The ESTs are useful in determining possible alternative splicing of the predicted genes ( Eyras et al. 2004 ). The methods used in predicting the Ensembl EST gene set are fully described elsewhere ( Eyras et al. 2004 ). Processed Pseudogene...
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Methods: ECgene: Genome-based EST clustering and gene modeling for alternative splicing
- Namshin Kim,
- Seokmin Shin,
- and Sanghyuk Lee
Genome Res. April 2005 15: 566-576; doi:10.1101/gr.3030405
...), available as one of the gene prediction tracks in the UCSC browser, each node is the splice site and the edges are exons or introns connecting the splice sites. Each node in the ESTgenes of the Ensembl system represents the sequence itself, and two types of edge indicate the inclusion and extension...
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RESOURCE: Genome-wide assembly and analysis of alternative transcripts in mouse
- Alexei A. Sharov,
- Dawood B. Dudekula,
- and Minoru S.H. Ko
Genome Res. May 2005 15: 748-754; doi:10.1101/gr.3269805
...in the human . Nat. Genet. 29 : 412 –417. ↵ Eyras, E., Caccamo, M., Curwen, V., and Clamp, M. 2004 . ESTGenes: Alternative splicing from ESTs in Ensembl. Genome Res. 14 : 976 –987. ↵ Galante, P.A., Sakabe, N.J., Kirschbaum-Slager, N., and de Souza, S.J. 2004 . Detection and evaluation of intron retention...
OPEN ACCESS ARTICLE
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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
...transcripts to improve those of higher confidence if necessary. The Gramene pipeline retains all high-confidence alternatively spliced transcripts based on the alignment score at the transcript level. In the original Ensembl pipeline, the number of predicted alternative splicing forms can become quite large...
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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
...of interest along with all other annotations provided by Ensembl and VectorBase browsers (e.g., gene models, ESTs, transcripts). This feature can be used for confirming or altering the gene models of the existing annotations. Figure 1. Flowchart illustrating the proteogenomics analysis steps. Genome Research...

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