Genome Biology

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This article is part of the supplement: EGASP '05: ENCODE Genome Annotation Assessment Project

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JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions

Jonathan E Allen, William H Majoros, Mihaela Pertea and Steven L Salzberg*

Genome Biology 2006, 7(Suppl 1):S9 doi:10.1186/gb-2006-7-s1-s9

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MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

Carson Holt, Mark Yandell BMC Bioinformatics 2011, 12:491 (22 December 2011)

Research Article   Open Access

A Metastate HMM with Application to Gene Structure Identification in Eukaryotes

Stephen Winters-Hilt, Carl Baribault EURASIP Journal on Advances in Signal Processing 2010, 2010:581373 (30 November 2010)

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Between a chicken and a grape: estimating the number of human genes

Mihaela Pertea, Steven L Salzberg Genome Biology 2010, 11:206 (5 May 2010)

This article is part of a collection on 10th Anniversary...

The number of genes in the human genome is still an estimate.

Research article   Open Access

nGASP – the nematode genome annotation assessment project

Avril Coghlan, Tristan J Fiedler, Sheldon J McKay, Paul Flicek, Todd W Harris, Darin Blasiar, Lincoln D Stein BMC Bioinformatics 2008, 9:549 (19 December 2008)

Methodology article   Open Access

Reranking candidate gene models with cross-species comparison for improved gene prediction

Qian Liu, Koby Crammer, Fernando CN Pereira, David S Roos BMC Bioinformatics 2008, 9:433 (14 October 2008)

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EGASP: the human ENCODE Genome Annotation Assessment Project

Roderic Guigó, Paul Flicek, Josep F Abril, Alexandre Reymond, Julien Lagarde, France Denoeud, Stylianos Antonarakis, Michael Ashburner, Vladimir B Bajic, Ewan Birney, Robert Castelo, Eduardo Eyras, Catherine Ucla, Thomas R Gingeras, Jennifer Harrow, Tim Hubbard, Suzanna E Lewis, Martin G Reese Genome Biology 2006, 7(Suppl 1):S2 (7 August 2006)