Introduction
Genome Biology 2006 7(Suppl 1):S1
Published on: 7 August 2006
Volume 7 Supplement 1
EGASP '05: ENCODE Genome Annotation Assessment Project
Research
Edited by Roderic Guigó, Martin G Reese
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Review
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...
Genome Biology 2006 7(Suppl 1):S2
Published on: 7 August 2006
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Review
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...
Genome Biology 2006 7(Suppl 1):S3
Published on: 7 August 2006
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Research
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...
Genome Biology 2006 7(Suppl 1):S4
Published on: 7 August 2006
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Research
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...
Genome Biology 2006 7(Suppl 1):S5
Published on: 7 August 2006
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Research
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...
Genome Biology 2006 7(Suppl 1):S6
Published on: 7 August 2006
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Research
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...
Genome Biology 2006 7(Suppl 1):S7
Published on: 7 August 2006
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Research
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...
Genome Biology 2006 7(Suppl 1):S8
Published on: 7 August 2006
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Research
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...
Genome Biology 2006 7(Suppl 1):S9
Published on: 7 August 2006
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Research
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...
Genome Biology 2006 7(Suppl 1):S10
Published on: 7 August 2006
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Research
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 ...
Genome Biology 2006 7(Suppl 1):S11
Published on: 7 August 2006
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Research
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...
Genome Biology 2006 7(Suppl 1):S12
Published on: 7 August 2006
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Research
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...
Genome Biology 2006 7(Suppl 1):S13
Published on: 7 August 2006
