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nGASP - the nematode genome annotation assessment project
2008
BMC Bioinformatics
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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
2009
Genome Research
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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
2010
Genome Biology
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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
2009
Bioinformatics
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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
2018
GigaScience
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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
2007
Nucleic Acids Research
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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]
2017
bioRxiv
pre-print
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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
2014
BMC Bioinformatics
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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
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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
2012
Development
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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
2014
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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
2010
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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]
2009
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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