ABSTRACT
We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.
Subject(s)
Genome, Viral , Genomics/methods , Virus Cultivation , Viruses/genetics , Viruses/isolation & purification , Databases, GeneticABSTRACT
Nucleotide and protein sequences are the foundation for all bioinformatics tools and resources. Researchers can analyze these sequences to discover genes or predict the function of their products. The INSDC (International Nucleotide Sequence Database-DDBJ/ENA/GenBank + SRA) is an international, centralized primary sequence resource that is freely available on the Internet. This database contains all publicly available nucleotide and derived protein sequences. This chapter discusses the structure and history of the nucleotide sequence database resources built at NCBI, provides information on how to submit sequences to the databases, and explains how to access the sequence data.
Subject(s)
High-Throughput Nucleotide Sequencing/methods , Computational Biology/methods , Databases, Genetic , Databases, Nucleic Acid , Genomics/methods , Sequence Analysis, DNA/methodsABSTRACT
The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases.
Subject(s)
Databases, Factual/standards , Information DisseminationABSTRACT
Nucleotide and protein sequences are the foundation for all bioinformatics tools and resources. Researchers can analyze these sequences to discover genes or predict the function of their products. The INSD (International Nucleotide Sequence Database--DDBJ/EMBL/GenBank) is an international, centralized primary sequence resource that is freely available on the internet. This database contains all publicly available nucleotide and derived protein sequences. This chapter summarizes the nucleotide sequence database resources, provides information on how to submit sequences to the databases, and explains how to access the sequence data.
Subject(s)
Databases, Nucleic Acid , Databases, Protein , InternetABSTRACT
The Third Party Annotation (TPA) project collects and presents high-quality annotation of nucleotide sequence. Annotation is submitted by researchers who have not themselves generated novel nucleotide sequence. In its first few years, the resource has proven to be popular with submitters from a range of biological research areas. Central to the project is the requirement for high-quality data, resulting from experimental and inferred analysis discussed in peer-reviewed publications. The data are divided into two tiers: those with experimental evidence and those with inferential evidence. Standards for TPA are detailed and illustrated with the aid of case studies.
