The Distributed Annotation System

Dowell, Robin D.; Jokerst, Rodney M.; Day, Allen; Eddy, Sean R.; Stein, Lincoln

doi:10.1186/1471-2105-2-7

Cited by 370 publications

(127 citation statements)

References 11 publications

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“…Using the Perl-based Proserver (Finn et al 2007), a Distributed Annotation System (Dowell et al 2001) (DAS) feature server was implemented that allows the identified peptides stored in the GenoMS-DB database (Fig. 1) to be visualized as tracks in various genome browsers and curation tools.…”

Section: Distributed Annotation Systemmentioning

confidence: 99%

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome

Brosch¹,

Saunders²,

Frankish³

et al. 2011

Genome Res.

118

125

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Recent advances in proteomic mass spectrometry (MS) offer the chance to marry high-throughput peptide sequencing to transcript models, allowing the validation, refinement, and identification of new protein-coding loci. We present a novel pipeline that integrates highly sensitive and statistically robust peptide spectrum matching with genome-wide protein-coding predictions to perform large-scale gene validation and discovery in the mouse genome for the first time. In searching an excess of 10 million spectra, we have been able to validate 32%, 17%, and 7% of all protein-coding genes, exons, and splice boundaries, respectively. Moreover, we present strong evidence for the identification of multiple alternatively spliced translations from 53 genes and have uncovered 10 entirely novel protein-coding genes, which are not covered in any mouse annotation data sources. One such novel protein-coding gene is a fusion protein that spans the Ins2 and Igf2 loci to produce a transcript encoding the insulin II and the insulin-like growth factor 2–derived peptides. We also report nine processed pseudogenes that have unique peptide hits, demonstrating, for the first time, that they are not just transcribed but are translated and are therefore resurrected into new coding loci. This work not only highlights an important utility for MS data in genome annotation but also provides unique insights into the gene structure and propagation in the mouse genome. All these data have been subsequently used to improve the publicly available mouse annotation available in both the Vega and Ensembl genome browsers (http://vega.sanger.ac.uk).

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Section: Distributed Annotation Systemmentioning

confidence: 99%

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome

Brosch¹,

Saunders²,

Frankish³

et al. 2011

Genome Res.

118

125

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“…Several web interface improvements and a distributed annotation system [25] server are in progress. Protein family classification is being investigated using machine learning and the diverse predictions that are available in Unison.…”

Section: Discussionmentioning

confidence: 99%

Unison: An Integrated Platform for Computational Biology Discovery

Hart¹,

Mukhyala

2008

Biocomputing 2009

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This paper describes the design and applications of Unison, a comprehensive and integrated warehouse of protein sequences, diverse precomputed predictions, and other biological data. Unison provides a practical solution to the burden of preparing data for computational discovery projects, enables holistic feature-based mining queries regarding protein composition and functions, and provides a foundation for the development of new tools. Unison is available for immediate use online via direct database connections and a web interface. In addition, the database schema, command line tools, web interface, and non-proprietary precomputed predictions are released under the Academic Free License and available for download at http://unison-db.org/. This project has resulted in a system that significantly reduces several practical impediments to the initiation of computational biology discovery projects.

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“…This service can be used for exploration of ligandbinding sites and small three-dimensional structural motifs across the entire PDB archive. PDBeMotif also integrates sequence-based annotation information using DAS technology (Dowell et al, 2001) and allows users to compare this information with annotations based on the three-dimensional structure. It is possible to examine the ligand-binding characteristics of a single protein or of groups of proteins based on classifications such as EC (Fleischmann et al, 2004), Pfam (Finn et al, 2010), CATH (Greene et al, 2007) and SCOP.…”

Section: Advanced Servicesmentioning

confidence: 99%

The Protein Data Bank in Europe (PDBe): bringing structure to biology

Velankar

Kleywegt

2011

Acta Crystallogr D Biol Cryst

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The Protein Data Bank in Europe (PDBe) is the European partner in the Worldwide PDB and as such handles depositions of X‐ray, NMR and EM data and structure models. PDBe also provides advanced bioinformatics services based on data from the PDB and related resources. Some of the challenges facing the PDB and its guardians are discussed, as well as some of the areas on which PDBe activities will focus in the future (advanced services, ligands, integration, validation and experimental data). Finally, some recent developments at PDBe are described.

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The Distributed Annotation System

Abstract: Background: Currently, most genome annotation is curated by centralized groups with limited resources. Efforts to share annotations transparently among multiple groups have not yet been satisfactory.

Cited by 370 publications

References 11 publications

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome

Unison: An Integrated Platform for Computational Biology Discovery

The Protein Data Bank in Europe (PDBe): bringing structure to biology

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