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NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

K. D. Pruitt, T. Tatusova, G. R. Brown, D. R. Maglott
2011 Nucleic Acids Research  
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  ...  The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of genomic, transcript and protein sequence records.  ...  INTRODUCTION RefSeq integrates an organisms' genomic, transcript and protein sequence with descriptive feature annotation and bibliographic information (1, 2) .  ... 
doi:10.1093/nar/gkr1079 pmid:22121212 pmcid:PMC3245008 fatcat:n2exzcnlwbfi7ef24fcdeyuaca

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

K. D. Pruitt, T. Tatusova, D. R. Maglott
2007 Nucleic Acids Research  
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, when additional data are available from those sources and therefore represent a current description of the sequence and its features.  ...  INTRODUCTION RefSeq is a public database of nucleotide and protein sequences with feature and bibliographic annotation.  ... 
doi:10.1093/nar/gkl842 pmid:17130148 pmcid:PMC1716718 fatcat:t7rciayrzncfnmxhdp44hjk76a

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Nuala A. O'Leary, Mathew W. Wright, J. Rodney Brister, Stacy Ciufo, Diana Haddad, Rich McVeigh, Bhanu Rajput, Barbara Robbertse, Brian Smith-White, Danso Ako-Adjei, Alexander Astashyn, Azat Badretdin (+43 others)
2015 Nucleic Acids Research  
The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature.  ...  The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http:/  ...  and accuracy of the represented sequence, structural annotation, and functional annotation.  ... 
doi:10.1093/nar/gkv1189 pmid:26553804 pmcid:PMC4702849 fatcat:2bm7d5coyvfotaj23hnj3mce6m

NCBI Reference Sequences: current status, policy and new initiatives

K. D. Pruitt, T. Tatusova, W. Klimke, D. R. Maglott
2009 Nucleic Acids Research  
RefSeq records integrate information from multiple sources and represent a current description of the sequence, the gene and sequence features.  ...  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.  ...  INTRODUCTION NCBI's Reference Sequence (RefSeq) is a public database of nucleotide and protein sequences with feature and bibliographic annotation.  ... 
doi:10.1093/nar/gkn721 pmid:18927115 pmcid:PMC2686572 fatcat:77xptvs54fghxb3dur3ykwycgq

RefSeq: an update on mammalian reference sequences

Kim D. Pruitt, Garth R. Brown, Susan M. Hiatt, Françoise Thibaud-Nissen, Alexander Astashyn, Olga Ermolaeva, Catherine M. Farrell, Jennifer Hart, Melissa J. Landrum, Kelly M. McGarvey, Michael R. Murphy, Nuala A. O'Leary (+17 others)
2013 Nucleic Acids Research  
The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of annotated genomic, transcript and protein sequence records derived from data in public sequence  ...  and novel exons annotated on mammalian RefSeq genomes.  ...  Cruz and the Wellcome Trust Sanger Institute for many fruitful discussions regarding correct genome annotation, gene location and nomenclature.  ... 
doi:10.1093/nar/gkt1114 pmid:24259432 pmcid:PMC3965018 fatcat:wid54lruqrdzndb4oghwltdrqa

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation

Shashikant Pujar, Nuala A O'Leary, Catherine M Farrell, Jane E Loveland, Jonathan M Mudge, Craig Wallin, Carlos G Girón, Mark Diekhans, If Barnes, Ruth Bennett, Andrew E Berry, Eric Cox (+25 others)
2017 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors wish to thank all programmers and other staff at NCBI, EMBL-EBI, UCSC, HGNC and MGI, who contributed to CCDS analyses and maintenance of the CCDS database and its internal  ...  The authors also thank UniProtKB curators, scientific experts and CCDS users for their helpful inputs. FUNDING  ...  These genome features were annotated as independent genes by NCBI (Annotation Release 108) and Ensembl (Release 85).  ... 
doi:10.1093/nar/gkx1031 pmid:29126148 pmcid:PMC5753299 fatcat:xlfpwnmezjejtbg7dyatdwspvi

Current status and new features of the Consensus Coding Sequence database

Catherine M. Farrell, Nuala A. O'Leary, Rachel A. Harte, Jane E. Loveland, Laurens G. Wilming, Craig Wallin, Mark Diekhans, Daniel Barrell, Stephen M. J. Searle, Bronwen Aken, Susan M. Hiatt, Adam Frankish (+31 others)
2013 Nucleic Acids Research  
mouse reference genome assemblies by the National Center for Biotechnology Information (NCBI) and Ensembl genome annotation pipelines.  ...  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.  ...  ACKNOWLEDGEMENTS The authors wish to thank the programmers, database and curation staff at Ensembl, NCBI, HAVANA and UCSC for their contributions to the CCDS analysis, maintenance and continuing curation  ... 
doi:10.1093/nar/gkt1059 pmid:24217909 pmcid:PMC3965069 fatcat:go2bm4timjdhzc6ecp42w77k7m

Tracking and coordinating an international curation effort for the CCDS Project

R. A. Harte, C. M. Farrell, J. E. Loveland, M.-M. Suner, L. Wilming, B. Aken, D. Barrell, A. Frankish, C. Wallin, S. Searle, M. Diekhans, J. Harrow (+1 others)
2012 Database: The Journal of Biological Databases and Curation  
mouse reference genome assemblies.  ...  Here, we present the current status of the CCDS database and details on our procedures to track and coordinate our efforts.  ...  Acknowledgements We wish to thank the programmers, database and curation staff at Ensembl, NCBI, WTSI and UCSC for their contribution to the CCDS analysis, maintenance and continuing curation efforts.  ... 
doi:10.1093/database/bas008 pmid:22434842 pmcid:PMC3308164 fatcat:3rppcgpcovf7deqvave3x3lafe

Microbial virus genome annotation—Mustering the troops to fight the sequence onslaught

J. Rodney Brister, Phillippe Le Mercier, James C. Hu
2012 Virology  
U24GM088849 and the NIH No. R01 GM089636.  ...  There are currently 4218 viral RefSeq genome records publicly available from NCBI.  ...  These ''reference proteomes'' are chosen from existing NCBI RefSeq genomes, so each reference has manually curated genome and proteome components and can be used as a gold standard (The UniProt Consortium  ... 
doi:10.1016/j.virol.2012.09.027 pmid:23084289 pmcid:PMC3518702 fatcat:3tfkd6gzbfa6nin2qgsn5cnwcq

Database resources of the National Center for Biotechnology Information

E. W. Sayers, T. Barrett, D. A. Benson, E. Bolton, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, S. Federhen, M. Feolo, I. M. Fingerman (+31 others)
2011 Nucleic Acids Research  
All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih. gov. † The members of the NCBI Resource Coordinators group are listed in the Appendix.  ...  PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and  ...  The Genome home page also provides links to an organism browser that lists the current status of all genomes annotated at NCBI.  ... 
doi:10.1093/nar/gkr1184 pmid:22140104 pmcid:PMC3245031 fatcat:zxmwupa435gfzcpusnv7oe3qnm

Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants

Jacqueline A. L. MacArthur, Joannella Morales, Ray E. Tully, Alex Astashyn, Laurent Gil, Elspeth A. Bruford, Pontus Larsson, Paul Flicek, Raymond Dalgleish, Donna R. Maglott, Fiona Cunningham
2013 Nucleic Acids Research  
Locus Reference Genomic (LRG; http://www.lrgsequence.org/) records contain internationally recognized stable reference sequences designed specifically for reporting clinically relevant sequence variants  ...  The fixed section contains stable genomic DNA sequence for a genomic region, essential transcripts and proteins for variant reporting and an exon numbering system.  ...  Whenever a new genome assembly is available, and the NCBI and Ensembl databases have been updated, the mapping information and annotation of all LRGs will be updated to the new assembly.  ... 
doi:10.1093/nar/gkt1198 pmid:24285302 pmcid:PMC3965024 fatcat:axjizdeznzg6rd5jaxuwo27zsu

Connecting Sequence and Biology in the Laboratory Mouse

R. M. Baldarelli
2003 Genome Research  
The Mouse Genome Sequencing Consortium and the RIKEN Genome Exploration Research group have generated large sets of sequence data representing the mouse genome and transcriptome, respectively.  ...  In this paper, we describe how the partnership of MGI and NCBI LocusLink contributes to the integration of sequence and biology, especially in the context of the large-scale genome and transcriptome data  ...  The integration of mouse biological data in MGI is possible only through their cooperative and dedicated efforts. We thank Leah Rae Donahue and Stanton Short for access to the  ... 
doi:10.1101/gr.991003 pmid:12819150 pmcid:PMC403701 fatcat:lp43pryrcfh2vfh22sjcy5l2hu

Database resources of the National Center for Biotechnology Information

D. L. Wheeler, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, R. Edgar, S. Federhen, L. Y. Geer, Y. Kapustin (+18 others)
2007 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other  ...  NCBI resources include  ...  DNA AND RNA Reference sequences The NCBI Reference Sequence (RefSeq) database (9) is a non-redundant set of curated and computationally derived sequences for transcripts, proteins and genomic regions  ... 
doi:10.1093/nar/gkl1031 pmid:17170002 pmcid:PMC1781113 fatcat:pj7gnwwlpnbmza7c4ae7yatega

Database Resources of the National Center for Biotechnology Information

2016 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other  ...  NCBI resources include  ...  DNA AND RNA Reference sequences The NCBI Reference Sequence (RefSeq) database (9) is a non-redundant set of curated and computationally derived sequences for transcripts, proteins and genomic regions  ... 
doi:10.1093/nar/gkw1071 pmid:27899561 pmcid:PMC5210554 fatcat:itaqk5uwv5bv7gm7f55zunbcwq

Database resources of the National Center for Biotechnology Information

E. W. Sayers, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, R. Edgar, S. Federhen, M. Feolo, L. Y. Geer (+21 others)
2009 Nucleic Acids Research  
A new Advanced Search option is available that reorganizes the current Limits and Preview/Index  ...  RECENT DEVELOPMENTS Enhancements to PubMed searches Over the past year, NCBI has introduced several enhancements to the PubMed search interface and Abstract Plus views.  ...  Reference Sequences. The NCBI Reference Sequence (RefSeq) database MMDB.  ... 
doi:10.1093/nar/gkn741 pmid:18940862 pmcid:PMC2686545 fatcat:wbtxaka7ibbbdn7xj2ga7n46ge
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