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nGASP - the nematode genome annotation assessment project

Avril Coghlan, Tristan J Fiedler, Sheldon J McKay, Paul Flicek, Todd W Harris, Darin Blasiar, The nGASP Consortium, Lincoln D Stein
2008 BMC Bioinformatics  
The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation  ...  of the genomes of four additional Caenorhabditis species and other nematodes.  ...  This work was supported in part by a grant from the National Human Genome Research Institute at the US National Institutes of Health # P41 HG02223. A.  ... 
doi:10.1186/1471-2105-9-549 pmid:19099578 pmcid:PMC2651883 fatcat:5pcpd3ultfegjlfd25jy4cqchi

mGene: Accurate SVM-based gene finding with an application to nematode genomes

G. Schweikert, A. Zien, G. Zeller, J. Behr, C. Dieterich, C. S. Ong, P. Philips, F. De Bona, L. Hartmann, A. Bohlen, N. Kruger, S. Sonnenburg (+1 others)
2009 Genome Research  
Finally, we also thank The Genome Center at Washington University School of Medicine in St.  ...  We thank the nGASP team for organizing the competition and Tristan Fiedler and Sheldon McKay in particular for their help with data sets and predictions.  ...  With mGene, we participated in the nematode genome annotation assessment project (nGASP) (Coghlan et al. 2008) .  ... 
doi:10.1101/gr.090597.108 pmid:19564452 pmcid:PMC2775605 fatcat:wpwffdyoefh3jo4aagmzmntcvm

A standard variation file format for human genome sequences

Martin G Reese, Barry Moore, Colin Batchelor, Fidel Salas, Fiona Cunningham, Gabor Marth, Lincoln Stein, Paul Flicek, Mark Yandell, Karen Eilbeck
2010 Genome Biology  
Here we describe the Genome Variation Format (GVF) and the 10Gen dataset.  ...  The 10Gen dataset, ten human genomes in GVF format, is freely available for community analysis from the Sequence Ontology website and from an Amazon elastic block storage (EBS) snapshot for use in Amazon's  ...  We also acknowledge the 1000 Genomes Project for making data publicly available.  ... 
doi:10.1186/gb-2010-11-8-r88 pmid:20796305 pmcid:PMC2945790 fatcat:75ifihv6jng73gsedpqcwwhvsi

Apollo: a community resource for genome annotation editing

E. Lee, N. Harris, M. Gibson, R. Chetty, S. Lewis
2009 Bioinformatics  
Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the community.  ...  Installers for Windows, Linux, Unix, Solaris and Mac OS X are available at http://apollo.berkeleybop.org, and the source code is available from the SourceForge CVS repository at  ...  fixes, Scott Cain and David Clements for GMOD support, help and documentation and the Apollo community for the continued support, user requests and help in finding bugs.  ... 
doi:10.1093/bioinformatics/btp314 pmid:19439563 pmcid:PMC2705230 fatcat:pbtlkvpsqbbx7kt4x47hwjpkra

Improving the annotation of the Heterorhabditis bacteriophora genome

Florence McLean, Duncan Berger, Dominik R Laetsch, Hillel T Schwartz, Mark Blaxter
2018 GigaScience  
Genome assembly and annotation remain exacting tasks.  ...  It is thus likely that methodological issues drove the apparent uniqueness of the initial H. bacteriophora genome annotation and that similar contamination and misannotation issues affect other published  ...  Adler Dillman provided the parental strain for the inbred H. bacteriophora strain G2a1223.  ... 
doi:10.1093/gigascience/giy034 pmid:29617768 pmcid:PMC5906903 fatcat:viqcczh7xbc7rh7qdjmbpodkb4

WormBase 2007

A. Rogers, I. Antoshechkin, T. Bieri, D. Blasiar, C. Bastiani, P. Canaran, J. Chan, W. J. Chen, P. Davis, J. Fernandes, T. J. Fiedler, M. Han (+21 others)
2007 Nucleic Acids Research  
Derived from the initial ACeDB database of C. elegans genetic and sequence information, WormBase now  ...  WormBase (www.wormbase.org) is the major publicly available database of information about Caenorhabditis elegans, an important system for basic biological and biomedical research.  ...  ACKNOWLEDGEMENTS WormBase is supported by grant P41-HG02223 from the US National Human Genome Research Institute and the British Medical Research Council.  ... 
doi:10.1093/nar/gkm975 pmid:17991679 pmcid:PMC2238927 fatcat:6hfq2jgvmfho5lbllbztcpxbvq

Improving the annotation of the Heterorhabditis bacteriophora genome [article]

Florence McLean, Duncan Berger, Dominik Laetsch, Hillel Schwartz, Mark Blaxter
2017 bioRxiv   pre-print
Genome assembly and annotation remains an exacting task.  ...  It is thus likely that methodological issues drove the apparent uniqueness of the initial H. bacteriophora genome annotation and that similar contamination and misannotation issues affect other published  ...  While JIGSAW achieved high sensitivity and specificity at the level of nucleotide, exon and gene predictions in the nematode genome annotation assessment project, nGASP [27] , direct comparison of the  ... 
doi:10.1101/225904 fatcat:zhwtiqvl6zdu5b2fil4cknf6um

SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models

Ian Reid, Nicholas O'Toole, Omar Zabaneh, Reza Nourzadeh, Mahmoud Dahdouli, Mostafa Abdellateef, Paul MK Gordon, Jung Soh, Gregory Butler, Christoph W Sensen, Adrian Tsang
2014 BMC Bioinformatics  
The pipeline has been developed and streamlined by comparing its predictions to manually curated gene models in three fungal genomes and validated against the high-quality gene annotation of Neurospora  ...  The source code for the SnowyOwl pipeline (in Python) and a web interface (in PHP) is freely available from http://sourceforge.net/projects/snowyowl/.  ...  Acknowledgements The authors would like to thank Nadeeza Ishmael for preparing RNA samples and the McGill University Genome Quebec Innovation Centre for sequencing them.  ... 
doi:10.1186/1471-2105-15-229 pmid:24980894 pmcid:PMC4084796 fatcat:nkyn325imrdjvaadpbaqigpzbu

A Comprehensive Review of Emerging Computational Methods for Gene Identification

2016 Journal of Information Processing Systems  
Although the first phase of the Encyclopedia of DNA Elements (ENCODE) project has been claimed to be complete, the annotation of the functional elements is far from being so.  ...  Gene identification is at the center of genomic studies.  ...  Another similarly comprehensive evaluation project, the Nematode Genome Annotation Assessment Project (NGASP) [149] , evaluates different types of gene finding programs on the C. elegans genome that has  ... 
doi:10.3745/jips.04.0023 fatcat:nuyjbnvatbaq7iavx5io62sbmi

Context-dependent function of a conserved translational regulatory module

Q. Liu, C. Stumpf, C. Thomas, M. Wickens, E. S. Haag
2012 Development  
The PUF family RNA-binding proteins FBF-1 and FBF-2 limit XX spermatogenesis by repressing the male-promoting proteins FEM-3 and GLD-1.  ...  The derived hermaphrodite of C. elegans has regulated spermatogenesis in an otherwise female body.  ...  MATERIALS AND METHODS Phylogenetic analysis Protein datasets for C. elegans, C. briggsae, C. remanei, C. brenneri and C. japonica were retrieved from the Nematode Genome Annotation Assessment Project  ... 
doi:10.1242/dev.070128 pmid:22399679 pmcid:PMC3308183 fatcat:mpmpqamcpbgodbqdjtvhui2buq

Tools and Techniques for Genome Annotation and Analysis

Carson Hinton Holt
2014
However, advances in annotation technology have not kept pace with genome sequencing, and annotation has become the major bottleneck for many genome projects (especially those with limited bioinformatics  ...  In response to the challenges facing second-generation genome projects, I have developed the annotation pipeline MAKER2 together with accessory software for downstream analysis and data management.  ...  Genome Biol 2006, 7:1 -31. 23. Coghlan A, Fiedler T, McKay S, Flicek P, Harris T, Blasiar D, the n GC, Stein L: nGASP -the nematode genome annotation assessment project.  ... 
doi:10.26053/0h-xcfx-3vg0 fatcat:b7lchjg4sreb5gfbkfcyunuqeq

Creating a genomic resource for Grosmannia clavigera

William Scott DiGuistini
2010
We have annotated the genome using the transcriptome resources (e.g. ESTs and RNA-seq) and computational (gene prediction software) data.  ...  We have developed genomic resources for Gc including: a) the whole genome sequence, b) expressed sequence tags (ESTs), and c) RNA-seq data.  ...  ,Blasiar, D., et al. (2008). nGASP -the nematode genome annotation assessment project. BMCBioinformatics, 9, 549. Collins, C. M., Murray, P. G., Denman, S., Morrissey, J.  ... 
doi:10.14288/1.0071085 fatcat:rqyjezxmanfcfeyefjk7uibube

Machine Learning for Genomic Sequence Analysis [article]

Soeren Sonnenburg, Technische Universität Berlin, Technische Universität Berlin, Gunnar Rätsch
2009
In the year 2008 alone, about 250 genomes will have been sequenced.  ...  With the development of novel sequencing technologies, the way has been paved for cost efficient, high-throughput whole genome sequencing.  ...  Using blat (Kent, 2002) we aligned them against the genomic DNA (release WS120). The alignment was used to confirm exons and introns.  ... 
doi:10.14279/depositonce-2055 fatcat:g3s7el5shrhvlj42jx7z5xdh4a