Overview
This super-track combines related tracks from the
ENCODE Gene Annotation Assessment Project (EGASP)
2005 Gene Prediction Workshop.
The goal of the workshop was to evaluate automatic methods for
gene annotation of the human genome, with a focus on protein-coding genes.
Predictions were evaluated in terms of their ability to
reproduce the high-quality manually assisted GENCODE gene annotations
and to predict novel transcripts.
The EGASP Full track shows gene predictions covering all
44 ENCODE regions submitted before the GENCODE annotations were released.
The EGASP Partial track shows gene predictions that cover
some of the ENCODE regions, submitted before the GENCODE release.
The EGASP Update track shows gene predictions that cover
all ENCODE regions, submitted after the GENCODE release.
These annotations were originally produced using the hg17 assembly.
The following gene predictions are included:
Credits
Click here for a complete list of people who participated in the
GENCODE project.
The following individuals and institutions provided the data for the subtracks
in this annotation:
-
AceView: Danielle and Jean Thierry-Mieg,
NCBI, National
Institutes of Health.
-
DOGFISH-C: David Carter, Informatics Dept.,
Wellcome Trust Sanger
Institute.
-
Ensembl: Stephen Searle, Wellcome Trust Sanger Institute (joint
Sanger/EBI project).
-
Exogean: Sarah Djebali, Dyogen Lab,
Ecole Normale
Supérieure (Paris, France).
-
ExonHunter: Tomas Vinar, Waterloo Bioinformatics, School of Computer Science,
University of Waterloo.
-
Fgenesh, Fgenesh++: Victor Solovyev,
Department of Computer Science,
Royal Holloway, London University.
-
GeneID-U12, SGP2-U12: Tyler Alioto,
Grup de Recerca en Informàtica Biomèdica
(GRIB) at
the Institut Municipal d'Investigació Mèdica (IMIM), Barcelona.
-
GeneMark: Mark Borodovsky, Alex Lomsadze and Alexander Lukashin,
Department of
Biology, Georgia Institute of Technology.
-
JIGSAW: Jonathan Allen, Steven Salzberg group, The Institute for
Genomic Research (TIGR)
and the Center for Bioinformatics and Computational Biology
(CBCB) at the
University of Maryland, College Park.
-
Pairagon/N-SCAN: Randall Brown, Laboratory for Computational Genomics, Washington University
in St. Louis.
-
SPIDA: Damian Keefe, Birney Group, EMBL-EBI.
-
Twinscan: Paul Flicek, Brent Lab,
Washington University
in St. Louis.
-
ACEScan: Gene Yeo, Crick-Jacobs Center for Computational Biology,
Salk Institute.
-
Augustus: Mario Stanke, Department of Bioinformatics, University of Göttingen,
Germany.
-
GeneZilla: William Majoros, Dept. of Bioinformatics, The Institute for
Genomic Research (TIGR).
-
SAGA: Sourav Chatterji, Lior Pachter lab,
Department of Mathematics, U.C. Berkeley.
References
Ashurst JL, Chen CK, Gilbert JG, Jekosch K, Keenan S, Meidl P, Searle SM,
Stalker J, Storey R, Trevanion S et al.
The Vertebrate Genome Annotation (Vega) database.
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D459-65.
Guigo R, Dermitzakis ET, Agarwal P, Ponting CP, Parra G, Reymond A, Abril JF,
Keibler E, Lyle R, Ucla C et al.
Comparison of mouse and human genomes followed by experimental
verification yields an estimated 1,019 additional genes.
Proc Natl Acad Sci U S A. 2003 Feb 4;100(3):1140-5.
Mouse Genome Sequencing Consortium.
Initial sequencing and comparative analysis of the mouse
genome. Nature. 2002 Dec 5;420(6915):520-62.
Reymond A, Marigo V, Yaylaoglu MB, Leoni A, Ucla C, Scamuffa N, Caccioppoli C, Dermitzakis ET, Lyle R, Banfi S et al.
Human chromosome 21 gene expression atlas in the mouse.
Nature. 2002 Dec 5;420(6915):582-6.
Reymond A, Camargo AA, Deutsch S, Stevenson BJ, Parmigiani RB, Ucla C, Bettoni F, Rossier C, Lyle R, Guipponi M et al.
Nineteen additional unpredicted transcripts from human
chromosome 21. Genomics. 2002 Jun;79(6):824-32.
Chatterji S, Pachter L.
Multiple organism gene finding by collapsed Gibbs sampling.
J Comput Biol. 2005 Jul-Aug;12(6):599-608.
Siepel A, Haussler D.
Computational identification of evolutionarily conserved
exons.
Proc. 8th Int'l Conf. on Research in Computational Molecular Biology.
2004;177-186.
Augustus
Stanke M, Waack S.
Gene prediction with a hidden Markov model and a new intron
submodel.
Bioinformatics. 2003;19(Suppl. 2):ii215-ii225.
Stanke M, Steinkamp R, Waack S, Morgenstern B.
AUGUSTUS: a web server for gene finding in eukaryotes.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W309-12.
FGenesh++
Solovyev VV.
"Statistical approaches in Eukaryotic gene prediction".
In Handbook of Statistical Genetics (eds. Balding D et al.)
(John Wiley & Sons, Inc., 2001). p. 83-127.
GeneID
Blanco E, Parra G, Guigó R.
"Using geneid to identify genes".
In Current Protocols in Bioinformatics, Unit 4.3. (eds. Baxevanis AD.)
(John Wiley & Sons, Inc., 2002).
Guigó R.
Assembling genes from predicted exons in linear time with
dynamic programming.
J Comput Biol. 1998 Winter;5(4):681-702.
Guigó R, Knudsen S, Drake N, Smith T.
Prediction of gene structure.
J Mol Biol. 1992 Jul 5;226(1):141-57.
Parra G, Blanco E, Guigó R.
GeneID in Drosophila.
Genome Res. 2000 Apr;10(4):511-5.
JIGSAW
Allen JE, Pertea M, Salzberg SL.
Computational gene prediction using multiple sources of
evidence.
Genome Res. 2004 Jan;14(1):142-8.
Allen JE, Salzberg SL.
JIGSAW: integration of multiple sources of evidence for gene
prediction.
Bioinformatics. 2005 Sep 15;21(18):3596-603.
SGP2
Guigó R, Dermitzakis ET, Agarwal P, Ponting CP, Parra G,
Reymond A, Abril JF, Keibler E, Lyle R, Ucla C et al.
Comparison of mouse and human genomes followed by experimental
verification yields an estimated 1,019 additional genes.
Proc Natl Acad Sci U S A. 2003 Feb 4;100(3):1140-5.
Parra G, Agarwal P, Abril JF, Wiehe T, Fickett JW, Guigó R.
Comparative gene prediction in human and mouse.
Genome Res. 2003 Jan;13(1):108-17.
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