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1.
Nucleic Acids Res ; 46(D1): D221-D228, 2018 01 04.
Artigo em Inglês | MEDLINE | ID: mdl-29126148

RESUMO

The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community.


Assuntos
Sequência Consenso , Bases de Dados Genéticas , Fases de Leitura Aberta , Animais , Curadoria de Dados/métodos , Curadoria de Dados/normas , Bases de Dados Genéticas/normas , Guias como Assunto , Humanos , Camundongos , Anotação de Sequência Molecular , National Library of Medicine (U.S.) , Estados Unidos , Interface Usuário-Computador
2.
Nucleic Acids Res ; 42(Database issue): D865-72, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24217909

RESUMO

The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies by the National Center for Biotechnology Information (NCBI) and Ensembl genome annotation pipelines. Identical annotations that pass quality assurance tests are tracked with a stable identifier (CCDS ID). Members of the collaboration, who are from NCBI, the Wellcome Trust Sanger Institute and the University of California Santa Cruz, provide coordinated and continuous review of the dataset to ensure high-quality CCDS representations. We describe here the current status and recent growth in the CCDS dataset, as well as recent changes to the CCDS web and FTP sites. These changes include more explicit reporting about the NCBI and Ensembl annotation releases being compared, new search and display options, the addition of biologically descriptive information and our approach to representing genes for which support evidence is incomplete. We also present a summary of recent and future curation targets.


Assuntos
Bases de Dados Genéticas , Proteínas/genética , Animais , Éxons , Genômica , Humanos , Internet , Camundongos , Anotação de Sequência Molecular , Análise de Sequência
3.
Nucleic Acids Res ; 31(16): 4864-73, 2003 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-12907729

RESUMO

The African trypanosome, Trypanosoma brucei, causes sleeping sickness in humans in sub-Saharan Africa. Here we report the sequence and analysis of the 1.1 Mb chromosome I, which encodes approximately 400 predicted genes organised into directional clusters, of which more than 100 are located in the largest cluster of 250 kb. A 160-kb region consists primarily of three gene families of unknown function, one of which contains a hotspot for retroelement insertion. We also identify five novel gene families. Indeed, almost 20% of predicted genes are members of families. In some cases, tandemly arrayed genes are 99-100% identical, suggesting an active process of amplification and gene conversion. One end of the chromosome consists of a putative bloodstream-form variant surface glycoprotein (VSG) gene expression site that appears truncated and degenerate. The other chromosome end carries VSG and expression site-associated genes and pseudogenes over 50 kb of subtelomeric sequence where, unusually, the telomere-proximal VSG gene is oriented away from the telomere. Our analysis includes the cataloguing of minor genetic variations between the chromosome I homologues and an estimate of crossing-over frequency during genetic exchange. Genetic polymorphisms are exceptionally rare in sequences located within and around the strand-switches between several gene clusters.


Assuntos
Cromossomos/genética , DNA de Protozoário/genética , Genes de Protozoários/genética , Trypanosoma brucei brucei/genética , Animais , Mapeamento Cromossômico , DNA de Protozoário/química , Repetições de Microssatélites/genética , Dados de Sequência Molecular , Polimorfismo Genético , Recombinação Genética , Análise de Sequência de DNA , Glicoproteínas Variantes de Superfície de Trypanosoma/genética
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