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1.  RefSeq microbial genomes database: new representation and annotation strategy 
Nucleic Acids Research  2013;42(D1):D553-D559.
The source of the microbial genomic sequences in the RefSeq collection is the set of primary sequence records submitted to the International Nucleotide Sequence Database public archives. These can be accessed through the Entrez search and retrieval system at http://www.ncbi.nlm.nih.gov/genome. Next-generation sequencing has enabled researchers to perform genomic sequencing at rates that were unimaginable in the past. Microbial genomes can now be sequenced in a matter of hours, which has led to a significant increase in the number of assembled genomes deposited in the public archives. This huge increase in DNA sequence data presents new challenges for the annotation, analysis and visualization bioinformatics tools. New strategies have been developed for the annotation and representation of reference genomes and sequence variations derived from population studies and clinical outbreaks.
doi:10.1093/nar/gkt1274
PMCID: PMC3965038  PMID: 24316578
2.  Virus Variation Resource—recent updates and future directions 
Nucleic Acids Research  2013;42(D1):D660-D665.
Virus Variation (http://www.ncbi.nlm.nih.gov/genomes/VirusVariation/) is a comprehensive, web-based resource designed to support the retrieval and display of large virus sequence datasets. The resource includes a value added database, a specialized search interface and a suite of sequence data displays. Virus-specific sequence annotation and database loading pipelines produce consistent protein and gene annotation and capture sequence descriptors from sequence records then map these metadata to a controlled vocabulary. The database supports a metadata driven, web-based search interface where sequences can be selected using a variety of biological and clinical criteria. Retrieved sequences can then be downloaded in a variety of formats or analyzed using a suite of tools and displays. Over the past 2 years, the pre-existing influenza and Dengue virus resources have been combined into a single construct and West Nile virus added to the resultant resource. A number of improvements were incorporated into the sequence annotation and database loading pipelines, and the virus-specific search interfaces were updated to support more advanced functions. Several new features have also been added to the sequence download options, and a new multiple sequence alignment viewer has been incorporated into the resource tool set. Together these enhancements should support enhanced usability and the inclusion of new viruses in the future.
doi:10.1093/nar/gkt1268
PMCID: PMC3965055  PMID: 24304891
3.  PAirwise Sequence Comparison (PASC) and Its Application in the Classification of Filoviruses 
Viruses  2012;4(8):1318-1327.
PAirwise Sequence Comparison (PASC) is a tool that uses genome sequence similarity to help with virus classification. The PASC tool at NCBI uses two methods: local alignment based on BLAST and global alignment based on Needleman-Wunsch algorithm. It works for complete genomes of viruses of several families/groups, and for the family of Filoviridae, it currently includes 52 complete genomes available in GenBank. It has been shown that BLAST-based alignment approach works better for filoviruses, and therefore is recommended for establishing taxon demarcation criteria. When more genome sequences with high divergence become available, these demarcations will most likely become more precise. The tool can compare new genome sequences of filoviruses with the ones already in the database, and propose their taxonomic classification.
doi:10.3390/v4081318
PMCID: PMC3446765  PMID: 23012628
Filoviridae; filovirus; ICTV; International Committee on Taxonomy of Viruses; National Center for Biotechnology Information; NCBI; PAirwise Sequence Comparison; PASC; virus classification; virus taxonomy
4.  Database resources of the National Center for Biotechnology Information 
Nucleic Acids Research  2011;40(D1):D13-D25.
In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
doi:10.1093/nar/gkr1184
PMCID: PMC3245031  PMID: 22140104
5.  BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata 
Nucleic Acids Research  2011;40(D1):D57-D63.
As the volume and complexity of data sets archived at NCBI grow rapidly, so does the need to gather and organize the associated metadata. Although metadata has been collected for some archival databases, previously, there was no centralized approach at NCBI for collecting this information and using it across databases. The BioProject database was recently established to facilitate organization and classification of project data submitted to NCBI, EBI and DDBJ databases. It captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. Concomitantly, the BioSample database is being developed to capture descriptive information about the biological samples investigated in projects. BioProject and BioSample records link to corresponding data stored in archival repositories. Submissions are supported by a web-based Submission Portal that guides users through a series of forms for input of rich metadata describing their projects and samples. Together, these databases offer improved ways for users to query, locate, integrate and interpret the masses of data held in NCBI's archival repositories. The BioProject and BioSample databases are available at http://www.ncbi.nlm.nih.gov/bioproject and http://www.ncbi.nlm.nih.gov/biosample, respectively.
doi:10.1093/nar/gkr1163
PMCID: PMC3245069  PMID: 22139929
6.  NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy 
Nucleic Acids Research  2011;40(D1):D130-D135.
The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of genomic, transcript and protein sequence records. These records are selected and curated from public sequence archives and represent a significant reduction in redundancy compared to the volume of data archived by the International Nucleotide Sequence Database Collaboration. The database includes over 16 000 organisms, 2.4 × 106 genomic records, 13 × 106 proteins and 2 × 106 RNA records spanning prokaryotes, eukaryotes and viruses (RefSeq release 49, September 2011). The RefSeq database is maintained by a combined approach of automated analyses, collaboration and manual curation to generate an up-to-date representation of the sequence, its features, names and cross-links to related sources of information. We report here on recent growth, the status of curating the human RefSeq data set, more extensive feature annotation and current policy for eukaryotic genome annotation via the NCBI annotation pipeline. More information about the resource is available online (see http://www.ncbi.nlm.nih.gov/RefSeq/).
doi:10.1093/nar/gkr1079
PMCID: PMC3245008  PMID: 22121212
7.  Solving the Problem: Genome Annotation Standards before the Data Deluge 
Standards in Genomic Sciences  2011;5(1):168-193.
The promise of genome sequencing was that the vast undiscovered country would be mapped out by comparison of the multitude of sequences available and would aid researchers in deciphering the role of each gene in every organism. Researchers recognize that there is a need for high quality data. However, different annotation procedures, numerous databases, and a diminishing percentage of experimentally determined gene functions have resulted in a spectrum of annotation quality. NCBI in collaboration with sequencing centers, archival databases, and researchers, has developed the first international annotation standards, a fundamental step in ensuring that high quality complete prokaryotic genomes are available as gold standard references. Highlights include the development of annotation assessment tools, community acceptance of protein naming standards, comparison of annotation resources to provide consistent annotation, and improved tracking of the evidence used to generate a particular annotation. The development of a set of minimal standards, including the requirement for annotated complete prokaryotic genomes to contain a full set of ribosomal RNAs, transfer RNAs, and proteins encoding core conserved functions, is an historic milestone. The use of these standards in existing genomes and future submissions will increase the quality of databases, enabling researchers to make accurate biological discoveries.
doi:10.4056/sigs.2084864
PMCID: PMC3236044  PMID: 22180819
8.  The Genomic Standards Consortium 
PLoS Biology  2011;9(6):e1001088.
A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic Standards Consortium (GSC), an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences.
doi:10.1371/journal.pbio.1001088
PMCID: PMC3119656  PMID: 21713030
9.  Cryptic splice sites and split genes 
Nucleic Acids Research  2011;39(14):5837-5844.
We describe a new program called cryptic splice finder (CSF) that can reliably identify cryptic splice sites (css), so providing a useful tool to help investigate splicing mutations in genetic disease. We report that many css are not entirely dormant and are often already active at low levels in normal genes prior to their enhancement in genetic disease. We also report a fascinating correlation between the positions of css and introns, whereby css within the exons of one species frequently match the exact position of introns in equivalent genes from another species. These results strongly indicate that many introns were inserted into css during evolution and they also imply that the splicing information that lies outside some introns can be independently recognized by the splicing machinery and was in place prior to intron insertion. This indicates that non-intronic splicing information had a key role in shaping the split structure of eukaryote genes.
doi:10.1093/nar/gkr203
PMCID: PMC3152350  PMID: 21470962
10.  Towards BioDBcore: a community-defined information specification for biological databases 
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.
doi:10.1093/database/baq027
PMCID: PMC3017395  PMID: 21205783
11.  Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9 
Standards in Genomic Sciences  2010;3(3):216-224.
This report summarizes the proceedings of the 9th workshop of the Genomic Standards Consortium (GSC), held at the J. Craig Venter Institute, Rockville, MD, USA. It was the first GSC workshop to have open registration and attracted over 90 participants. This workshop featured sessions that provided overviews of the full range of ongoing GSC projects. It included sessions on Standards in Genomic Sciences, the open access journal of the GSC, building standards for genome annotation, the M5 platform for next-generation collaborative computational infrastructures, building ties with the biodiversity research community and two discussion panels with government and industry participants. Progress was made on all fronts, and major outcomes included the completion of the MIENS specification for publication and the formation of the Biodiversity working group.
doi:10.4056/sigs.1353455
PMCID: PMC3035308  PMID: 21304722
12.  Entrez Gene: gene-centered information at NCBI 
Nucleic Acids Research  2010;39(Database issue):D52-D57.
Entrez Gene (http://www.ncbi.nlm.nih.gov/gene) is National Center for Biotechnology Information (NCBI)’s database for gene-specific information. Entrez Gene maintains records from genomes which have been completely sequenced, which have an active research community to submit gene-specific information, or which are scheduled for intense sequence analysis. The content represents the integration of curation and automated processing from NCBI’s Reference Sequence project (RefSeq), collaborating model organism databases, consortia such as Gene Ontology and other databases within NCBI. Records in Entrez Gene are assigned unique, stable and tracked integers as identifiers. The content (nomenclature, genomic location, gene products and their attributes, markers, phenotypes and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is available via interactive browsing through NCBI’s Entrez system, via NCBI’s Entrez programming utilities (E-Utilities) and for bulk transfer by FTP.
doi:10.1093/nar/gkq1237
PMCID: PMC3013746  PMID: 21115458
13.  Database resources of the National Center for Biotechnology Information 
Nucleic Acids Research  2010;39(Database issue):D38-D51.
In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
doi:10.1093/nar/gkq1172
PMCID: PMC3013733  PMID: 21097890
14.  Towards BioDBcore: a community-defined information specification for biological databases 
Nucleic Acids Research  2010;39(Database issue):D7-D10.
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.
doi:10.1093/nar/gkq1173
PMCID: PMC3013734  PMID: 21097465
15.  Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop 
Viruses  2010;2(10):2258-2268.
Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world’s biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing sequence, function, and metadata annotation standards for viral genomes. This report describes the issues involved in viral genome annotation and reviews policy recommendations presented at the NCBI Annotation Workshop.
doi:10.3390/v2102258
PMCID: PMC3185566  PMID: 21994619
virus; genome; annotation
16.  Meeting Report: “Metagenomics, Metadata and Meta-analysis” (M3) Workshop at the Pacific Symposium on Biocomputing 2010 
Standards in Genomic Sciences  2010;2(3):357-360.
This report summarizes the M3 Workshop held at the January 2010 Pacific Symposium on Biocomputing. The workshop, organized by Genomic Standards Consortium members, included five contributed talks, a series of short presentations from stakeholders in the genomics standards community, a poster session, and, in the evening, an open discussion session to review current projects and examine future directions for the GSC and its stakeholders.
doi:10.4056/sigs.802738
PMCID: PMC3035291  PMID: 21304719
17.  Database resources of the National Center for Biotechnology Information 
Nucleic Acids Research  2009;38(Database issue):D5-D16.
In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, Reference Sequence, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Peptidome, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
doi:10.1093/nar/gkp967
PMCID: PMC2808881  PMID: 19910364
18.  Mining the NCBI Influenza Sequence Database: adaptive grouping of BLAST results using precalculated neighbor indexing 
PLoS Currents  2009;1:RRN1124.
The Influenza Virus Resource and other Virus Variation Resources at NCBI provide enhanced visualization web tools for exploratory analysis for influenza sequence data. Despite the improvements in data analysis, the initial data retrieval remains unsophisticated, frequently producing huge and imbalanced datasets due to the large number of identical and nearly-identical sequences in the database.
We propose a data mining algorithm to organize reported sequences into groups based on their relatedness to the query sequence and to each other. The algorithm uses BLAST to find database sequences related to the query. Neighbor lists precalculated from pairwise BLAST alignments between database sequences are used to organize results in groups of nearly-identical and strongly related sequences. We propose to use a non-symmetric dissimilarity measure well crafted for dealing with sequences of different length (fragments).
A balanced and representative data set produced by this tool can be used for further analysis, i.e. multiple sequence alignment and phylogenetic trees. The algorithm is implemented for protein coding sequences and is being integrated with the NCBI Influenza Virus Resource.
doi:10.1371/currents.RRN1124
PMCID: PMC2771650  PMID: 20029662
19.  Mining the NCBI Influenza Sequence Database: adaptive grouping of BLAST results using precalculated neighbor indexing 
PLoS Currents  2009;1:RRN1124.
The Influenza Virus Resource and other Virus Variation Resources at NCBI provide enhanced visualization web tools for exploratory analysis for influenza sequence data. Despite the improvements in data analysis, the initial data retrieval remains unsophisticated, frequently producing huge and imbalanced datasets due to the large number of identical and nearly-identical sequences in the database.
We propose a data mining algorithm to organize reported sequences into groups based on their relatedness to the query sequence and to each other. The algorithm uses BLAST to find database sequences related to the query. Neighbor lists precalculated from pairwise BLAST alignments between database sequences are used to organize results in groups of nearly-identical and strongly related sequences. We propose to use a non-symmetric dissimilarity measure well crafted for dealing with sequences of different length (fragments).
A balanced and representative data set produced by this tool can be used for further analysis, i.e. multiple sequence alignment and phylogenetic trees. The algorithm is implemented for protein coding sequences and is being integrated with the NCBI Influenza Virus Resource.
doi:10.1371/currents.RRN1124
PMCID: PMC2771650  PMID: 20029662
20.  Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta) genomic Annotation 
Abstract
The methodologies used to generate genome and metagenome annotations are diverse and vary between groups and laboratories. Descriptions of the annotation process are helpful in interpreting genome annotation data. Some groups have produced Standard Operating Procedures (SOPs) that describe the annotation process, but standards are lacking for structure and content of these descriptions. In addition, there is no central repository to store and disseminate procedures and protocols for genome annotation. We highlight the importance of SOPs for genome annotation and endorse an online repository of SOPs.
doi:10.1089/omi.2008.0017
PMCID: PMC3196215  PMID: 18416670
22.  Virus variation resources at the National Center for Biotechnology Information: dengue virus 
BMC Microbiology  2009;9:65.
Background
There is an increasing number of complete and incomplete virus genome sequences available in public databases. This large body of sequence data harbors information about epidemiology, phylogeny, and virulence. Several specialized databases, such as the NCBI Influenza Virus Resource or the Los Alamos HIV database, offer sophisticated query interfaces along with integrated exploratory data analysis tools for individual virus species to facilitate extracting this information. Thus far, there has not been a comprehensive database for dengue virus, a significant public health threat.
Results
We have created an integrated web resource for dengue virus. The technology developed for the NCBI Influenza Virus Resource has been extended to process non-segmented dengue virus genomes. In order to allow efficient processing of the dengue genome, which is large in comparison with individual influenza segments, we developed an offline pre-alignment procedure which generates a multiple sequence alignment of all dengue sequences. The pre-calculated alignment is then used to rapidly create alignments of sequence subsets in response to user queries. This improvement in technology will also facilitate the incorporation of additional virus species in the future. The set of virus-specific databases at NCBI, which will be referred to as Virus Variation Resources (VVR), allow users to build complex queries against virus-specific databases and then apply exploratory data analysis tools to the results. The metadata is automatically collected where possible, and extended with data extracted from the literature.
Conclusion
The NCBI Dengue Virus Resource integrates dengue sequence information with relevant metadata (sample collection time and location, disease severity, serotype, sequenced genome region) and facilitates retrieval and preliminary analysis of dengue sequences using integrated web analysis and visualization tools.
doi:10.1186/1471-2180-9-65
PMCID: PMC2675532  PMID: 19341451
23.  The National Center for Biotechnology Information's Protein Clusters Database 
Nucleic Acids Research  2008;37(Database issue):D216-D223.
Rapid increases in DNA sequencing capabilities have led to a vast increase in the data generated from prokaryotic genomic studies, which has been a boon to scientists studying micro-organism evolution and to those who wish to understand the biological underpinnings of microbial systems. The NCBI Protein Clusters Database (ProtClustDB) has been created to efficiently maintain and keep the deluge of data up to date. ProtClustDB contains both curated and uncurated clusters of proteins grouped by sequence similarity. The May 2008 release contains a total of 285 386 clusters derived from over 1.7 million proteins encoded by 3806 nt sequences from the RefSeq collection of complete chromosomes and plasmids from four major groups: prokaryotes, bacteriophages and the mitochondrial and chloroplast organelles. There are 7180 clusters containing 376 513 proteins with curated gene and protein functional annotation. PubMed identifiers and external cross references are collected for all clusters and provide additional information resources. A suite of web tools is available to explore more detailed information, such as multiple alignments, phylogenetic trees and genomic neighborhoods. ProtClustDB provides an efficient method to aggregate gene and protein annotation for researchers and is available at http://www.ncbi.nlm.nih.gov/sites/entrez?db=proteinclusters.
doi:10.1093/nar/gkn734
PMCID: PMC2686591  PMID: 18940865
24.  Database resources of the National Center for Biotechnology Information 
Nucleic Acids Research  2008;37(Database issue):D5-D15.
In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
doi:10.1093/nar/gkn741
PMCID: PMC2686545  PMID: 18940862
25.  NCBI Reference Sequences: current status, policy and new initiatives 
Nucleic Acids Research  2008;37(Database issue):D32-D36.
NCBI's Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. RefSeq records integrate information from multiple sources and represent a current description of the sequence, the gene and sequence features. The database includes over 5300 organisms spanning prokaryotes, eukaryotes and viruses, with records for more than 5.5 × 106 proteins (RefSeq release 30). Feature annotation is applied by a combination of curation, collaboration, propagation from other sources and computation. We report here on the recent growth of the database, recent changes to feature annotations and record types for eukaryotic (primarily vertebrate) species and policies regarding species inclusion and genome annotation. In addition, we introduce RefSeqGene, a new initiative to support reporting variation data on a stable genomic coordinate system.
doi:10.1093/nar/gkn721
PMCID: PMC2686572  PMID: 18927115

Results 1-25 (49)