EGASP: Introduction

Authors: Martin G Reese and Roderic Guigó

EGASP: the human ENCODE Genome Annotation Assessment Project

We present the results of EGASP, a community experiment to assess the state-of-the-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major g...

Authors: 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…

Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment

This study analyzes the predictions of a number of promoter predictors on the ENCODE regions of the human genome as part of the ENCODE Genome Annotation Assessment Project (EGASP). The systems analyzed operate...

Authors: Vladimir B Bajic, Michael R Brent, Randall H Brown, Adam Frankish, Jennifer Harrow, Uwe Ohler, Victor V Solovyev and Sin Lam Tan

GENCODE: producing a reference annotation for ENCODE

The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental valida...

Authors: Jennifer Harrow, France Denoeud, Adam Frankish, Alexandre Reymond, Chao-Kung Chen, Jacqueline Chrast, Julien Lagarde, James GR Gilbert, Roy Storey, David Swarbreck, Colette Rossier, Catherine Ucla, Tim Hubbard, Stylianos E Antonarakis and Roderic Guigo

Pairagon+N-SCAN_EST: a model-based gene annotation pipeline

This paper describes Pairagon+N-SCAN_EST, a gene annotation pipeline that uses only native alignments. For each expressed sequence it chooses the best genomic alignment. Systems like ENSEMBL and ExoGean rely on t...

Authors: Manimozhiyan Arumugam, Chaochun Wei, Randall H Brown and Michael R Brent

Vertebrate gene finding from multiple-species alignments using a two-level strategy

One way in which the accuracy of gene structure prediction in vertebrate DNA sequences can be improved is by analyzing alignments with multiple related species, since functional regions of genes tend to be mor...

Authors: David Carter and Richard Durbin

Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA

Accurate and automatic gene identification in eukaryotic genomic DNA is more than ever of crucial importance to efficiently exploit the large volume of assembled genome sequences available to the community. Au...

Authors: Sarah Djebali, Franck Delaplace and Hugues Roest Crollius

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts

As part of the ENCODE Genome Annotation Assessment Project (EGASP), we developed the MARS extension to the Twinscan algorithm. MARS is designed to find human alternatively spliced transcripts that are conserve...

Authors: Paul Flicek and Michael R Brent

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

Predicting complete protein-coding genes in human DNA remains a significant challenge. Though a number of promising approaches have been investigated, an ideal suite of tools has yet to emerge that can provide...

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

Automatic annotation of eukaryotic genes, pseudogenes and promoters

The ENCODE gene prediction workshop (EGASP) has been organized to evaluate how well state-of-the-art automatic gene finding methods are able to reproduce the manual and experimental gene annotation of the huma...

Authors: Victor Solovyev, Peter Kosarev, Igor Seledsov and Denis Vorobyev

AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome

A large number of gene prediction programs for the human genome exist. These annotation tools use a variety of methods and data sources. In the recent ENCODE genome annotation assessment project (EGASP), some ...

Authors: Mario Stanke, Ana Tzvetkova and Burkhard Morgenstern

AceView: a comprehensive cDNA-supported gene and transcripts annotation

Regions covering one percent of the genome, selected by ENCODE for extensive analysis, were annotated by the HAVANA/Gencode group with high quality transcripts, thus defining a benchmark. The ENCODE Genome Ann...

Authors: Danielle Thierry-Mieg and Jean Thierry-Mieg

A computational approach for identifying pseudogenes in the ENCODE regions

Pseudogenes are inheritable genetic elements showing sequence similarity to functional genes but with deleterious mutations. We describe a computational pipeline for identifying them, which in contrast to prev...

Authors: Deyou Zheng and Mark B Gerstein