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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)
<span title="2015-11-08">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
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:/  ...  The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature.  ...  and accuracy of the represented sequence, structural annotation, and functional annotation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv1189">doi:10.1093/nar/gkv1189</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26553804">pmid:26553804</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4702849/">pmcid:PMC4702849</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2bm7d5coyvfotaj23hnj3mce6m">fatcat:2bm7d5coyvfotaj23hnj3mce6m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190219055156/http://pdfs.semanticscholar.org/16b0/744424f02e01fe2f01b3ea03e2862f1359fc.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/16/b0/16b0744424f02e01fe2f01b3ea03e2862f1359fc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv1189"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702849" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

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)
<span title="2013-11-19">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
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  ...  We also describe a revised protein annotation policy for alternatively spliced transcripts with more divergent predicted proteins and we summarize the current status of the RefSeqGene project.  ...  ACKNOWLEDGEMENTS We thank our collaborators, especially the HUGO Gene Nomenclature Committee, the Mouse Genome Database, Rat Genome Database, UniProt and CCDS curators at the University of California Santa  ... 
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NCBI Reference Sequences: current status, policy and new initiatives

K. D. Pruitt, T. Tatusova, W. Klimke, D. R. Maglott
<span title="2009-01-01">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
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.  ...  INTRODUCTION NCBI's Reference Sequence (RefSeq) is a public database of nucleotide and protein sequences with feature and bibliographic annotation.  ... 
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BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata

T. Barrett, K. Clark, R. Gevorgyan, V. Gorelenkov, E. Gribov, I. Karsch-Mizrachi, M. Kimelman, K. D. Pruitt, S. Resenchuk, T. Tatusova, E. Yaschenko, J. Ostell
<span title="2011-12-01">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
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.  ...  As the volume and complexity of data sets archived at NCBI grow rapidly, so does the need to gather and organize the associated metadata.  ...  We also wish to thank the many NCBI staff members who have contributed to discussions and provided data or feedback on these resources, in particu- Conflict of interest statement. None declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr1163">doi:10.1093/nar/gkr1163</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22139929">pmid:22139929</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3245069/">pmcid:PMC3245069</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xjhql7u355bqtfmkq3ba2vtzjq">fatcat:xjhql7u355bqtfmkq3ba2vtzjq</a> </span>
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Mouse genome annotation by the RefSeq project

Kelly M. McGarvey, Tamara Goldfarb, Eric Cox, Catherine M. Farrell, Tripti Gupta, Vinita S. Joardar, Vamsi K. Kodali, Michael R. Murphy, Nuala A. O'Leary, Shashikant Pujar, Bhanu Rajput, Sanjida H. Rangwala (+5 others)
<span title="2015-07-28">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2wcheulsyvd7bott7zn35dhoti" style="color: black;">Mammalian Genome</a> </i> &nbsp;
Complete and accurate annotation of the mouse genome is critical to the advancement of research conducted on this important model organism.  ...  We thank our collaborators, especially the HUGO Gene Nomenclature Committee, the Mouse Genome Database, Rat Genome Database, UniProt and CCDS curators at the University of California Santa Cruz and the  ...  Acknowledgments We would like to recognize Francoise Thibaud-Nissen for providing the overview graphic depicting NCBI's eukaryotic genome annotation pipeline and statistics from the annotation releases  ... 
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Type material in the NCBI Taxonomy Database

Scott Federhen
<span title="2014-11-14">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The NCBI Taxonomy Database (http: //www.ncbi.nlm.nih.gov/taxonomy) now includes annotation of type material that we use to flag sequences from type in GenBank and in Genomes.  ...  Type material is the taxonomic device that ties formal names to the physical specimens that serve as exemplars for the species.  ...  Information about sequenced genomes at NCBI is currently maintained in our Assembly database.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku1127">doi:10.1093/nar/gku1127</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25398905">pmid:25398905</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4383940/">pmcid:PMC4383940</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mvhne3nzlvfk7lndskpvy7ckf4">fatcat:mvhne3nzlvfk7lndskpvy7ckf4</a> </span>
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RefSeq curation and annotation of antizyme and antizyme inhibitor genes in vertebrates

Bhanu Rajput, Terence D. Murphy, Kim D. Pruitt
<span title="2015-07-13">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Our goal was to provide an accurately curated and annotated Reference Sequence (RefSeq) data set of antizyme transcript and protein records across a broad taxonomic scope that would serve as standards  ...  Conventional computational tools are unable to predict a programmed frameshift, resulting in misannotation of antizyme transcripts and proteins on transcript and genomic sequences.  ...  INTRODUCTION The Reference Sequence (RefSeq) database at the National Center for Biotechnology Information (NCBI) is a collection of annotated genomic, transcript and protein sequence records for genomes  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv713">doi:10.1093/nar/gkv713</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26170238">pmid:26170238</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4551939/">pmcid:PMC4551939</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hou3eb5l6rdmxj4ptfxwkurvu4">fatcat:hou3eb5l6rdmxj4ptfxwkurvu4</a> </span>
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Clone DB: an integrated NCBI resource for clone-associated data

Valerie A. Schneider, Hsiu-Chuan Chen, Cliff Clausen, Peter A. Meric, Zhigang Zhou, Nathan Bouk, Nora Husain, Donna R. Maglott, Deanna M. Church
<span title="2012-11-26">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Clone DB represents an expansion and replacement of the former NCBI Clone Registry and has records for genomic and cell-based libraries and clones representing more than 100 different eukaryotic taxa.  ...  Clone DB is indexed in the NCBI Entrez system and can be queried by fields that include organism, clone name, gene name and sequence identifier.  ...  ACKNOWLEDGEMENTS The authors would like to thank Greg Schuler for his helpful insight and discussions of the Clone Registry and suggestions associated with clone name regularization and clone placements  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks1164">doi:10.1093/nar/gks1164</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23193260">pmid:23193260</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3531087/">pmcid:PMC3531087</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gyklpu73tjh5ji4tpgmuncnmaq">fatcat:gyklpu73tjh5ji4tpgmuncnmaq</a> </span>
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

C. L. Schoch, B. Robbertse, V. Robert, D. Vu, G. Cardinali, L. Irinyi, W. Meyer, R. H. Nilsson, K. Hughes, A. N. Miller, P. M. Kirk, K. Abarenkov (+89 others)
<span title="2014-06-30">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible  ...  In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi.  ...  A number of ITS sequences were re-annotated and formatted in a separate curated database at NCBI, RefSeq Targeted Loci (RTL).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bau061">doi:10.1093/database/bau061</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24980130">pmid:24980130</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4075928/">pmcid:PMC4075928</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oqjotp6vvzbrtdddii6nc67zy4">fatcat:oqjotp6vvzbrtdddii6nc67zy4</a> </span>
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Improving taxonomic accuracy for fungi in public sequence databases: applying 'one name one species' in well-defined genera with Trichoderma/Hypocrea as a test case

Barbara Robbertse, Pooja K Strope, Priscila Chaverri, Romina Gazis, Stacy Ciufo, Michael Domrachev, Conrad L Schoch
<span title="2017-01-01">2017</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
As a result, the ITS RefSeq Targeted Loci database at NCBI has been augmented with more sequences from type and verified material from Trichoderma species.  ...  Abstract The ITS (nuclear ribosomal internal transcribed spacer) RefSeq database at the National Center for Biotechnology Information (NCBI) is dedicated to the clear association between name, specimen  ...  Acknowledgements We thank the input of experts in the Trichoderma community as well the work by members of the International Subcommission on Trichoderma and Hypocrea (ISTH) as part of the International  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bax072">doi:10.1093/database/bax072</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29220466">pmid:29220466</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5641268/">pmcid:PMC5641268</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/t4oypzpx4nfatl3avfhn44u5ka">fatcat:t4oypzpx4nfatl3avfhn44u5ka</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210173223/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5641268&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5c/de/5cde9cceeb8669feb4a3a8ec12e849846c02da14.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bax072"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5641268" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Online Databases for Taxonomy and Identification of Pathogenic Fungi and Proposal for a Cloud-Based Dynamic Data Network Platform

Peralam Yegneswaran Prakash, Laszlo Irinyi, Catriona Halliday, Sharon Chen, Vincent Robert, Wieland Meyer, Colleen Suzanne Kraft
<span title="2017-02-08">2017</span> <i title="American Society for Microbiology"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fmv6b6fbubcnxficge3yz52hxa" style="color: black;">Journal of Clinical Microbiology</a> </i> &nbsp;
This minireview aims to provide an overview of currently available online databases for the taxonomy and identification of human and animal-pathogenic fungi and calls for the establishment of a cloud-based  ...  Thus, well-curated fungal databases with substantial accurate sequence data play a pivotal role for further research and diagnostics in the field of mycology.  ...  UNITE is extensively linked by means of cross-references and linkouts with the NCBI GenBank, NCBI RefSeq, and ISHAM-ITS databases (Fig. 2) , and as a result, it holds various fungal ITS sequences of pathogenic  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/jcm.02084-16">doi:10.1128/jcm.02084-16</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28179406">pmid:28179406</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5377827/">pmcid:PMC5377827</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6gjagj4o2fewrbyrg6bteyk2xu">fatcat:6gjagj4o2fewrbyrg6bteyk2xu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722235633/http://jcm.asm.org/content/55/4/1011.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4a/c3/4ac3ee2860d2e0603c41cd2e3f581d219f25d82c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/jcm.02084-16"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> asm.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5377827" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

COG database update: focus on microbial diversity, model organisms, and widespread pathogens

Michael Y Galperin, Yuri I Wolf, Kira S Makarova, Roberto Vera Alvarez, David Landsman, Eugene V Koonin
<span title="2020-11-09">2020</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
GenBank\ENA\DDBJ coding sequence (CDS) accession numbers; (ii) COG annotations are updated for &gt;200 newly characterized protein families with corresponding references and PDB links, where available;  ...  The current update, available at https://www.ncbi.nlm.nih.gov/research/COG, substantially expands the scope of the database to include complete genomes of 1187 bacteria and 122 archaea, typically, with  ...  Second, we added representatives of newly sequenced bacterial and archaeal genera, including those with the Candidatus status.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkaa1018">doi:10.1093/nar/gkaa1018</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33167031">pmid:33167031</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4c77x5ponfht5im2v4pu76byli">fatcat:4c77x5ponfht5im2v4pu76byli</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201110232612/https://watermark.silverchair.com/gkaa1018.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAArcwggKzBgkqhkiG9w0BBwagggKkMIICoAIBADCCApkGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMxKGfIOGsMgJZ-6JzAgEQgIICatl35H5DQ8T3H7UyhF10S1rli9K_Mbk6WPt0l5JZX10b3-zz-WuocnH9LxRnLqlOZyqBPPK1YtC5X0hWzH8S_cW_31LcN57IBNj0e0WAcymYBZAGw-e-iqr27QGXxjNC5hgRe16fUq8Cwpx9EampL6U-y70hrUdzWSz5vu8g4awMfVOJL_0QCXfVSxeQr0pxF5caruY1E_jOSYZlxtNtGY_dPleDl5WkBmPUBKF9kT1X3-D3gCocHyL_vl05cvEFfYNCgpx7VHtA1Jmxkzp1pB3dcwHEzKH_qmFqNWsm9walTYYypiUiGsaOv9dKni_0iAJV9IflCFHxWSgcUap30S2A7m773jjY47bpTlI4m0wXYxT-4SBsyOfP2ES6DfZ7b8W3UO-L_10TTwuTdI23H9UIQU9MVi2yAuApxCBYbsCEAYR0Bks5jU2LytZJ3KnbDbw6RqNKqzAlSOMBNIGdC_Ktp4FVWrTo2AXVVtzsELuIILJmlBDbQ-ERaUbN-u2wS0vumbDuvIVs7Ir2cqUJ4eDLCht26Z1fy6Zg-OmqaCciib0K7vCODWY457YW69qeSqgbxpNENWdeDvlHM9Te3QFzrcv6lMoNzPdz3gYBFKIF0SRzK8A0Lx22zuexy1hGLt0HthcIC2uacna14CqaszGx_0nWg6E63nKs4zUnTb7TTwo9jrac-Dzk73ZoYEp4cab3kkPwub97gw2WWlzM7nf7Bjsg3_9o6DAkoEURwuukMAwF89mCDvoyDQLnNh3uSe-iBAk3omkdSJRNjnj_LYhUXA4lRuF_4ymtkLBZqkB-XbVeNvcWkMNFXQ" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/20/20/20204090317b1a56c5c6b3013eb356fdfd5ee413.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkaa1018"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a>

Database resources of the National Center for Biotechnology Information

Eric W Sayers, Richa Agarwala, Evan E Bolton, J Rodney Brister, Kathi Canese, Karen Clark, Ryan Connor, Nicolas Fiorini, Kathryn Funk, Timothy Hefferon, J Bradley Holmes, Sunghwan Kim (+11 others)
<span title="2018-11-05">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank ® nucleic acid sequence database and the PubMed  ...  All of these resources can be accessed through the NCBI home page at www.ncbi. nlm.nih.gov.  ...  ACKNOWLEDGEMENTS The authors would like to thank all of the NCBI staff who through their dedicated efforts continue to allow NCBI to provide our full collection of services to the community.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky1069">doi:10.1093/nar/gky1069</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30395293">pmid:30395293</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6myevv752rbsjkfofodo4lo3gu">fatcat:6myevv752rbsjkfofodo4lo3gu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190228172850/http://pdfs.semanticscholar.org/8f43/f5972ce44b9571bb75226d1c12f24bd619ba.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8f/43/8f43f5972ce44b9571bb75226d1c12f24bd619ba.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky1069"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a>

KusakiDB v1.0: a novel approach for validation and completeness of protein orthologous groups [article]

Andrea Ghelfi, Yasukazu Nakamura, Sachiko Isobe
<span title="2020-11-10">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Therefore, we created KusakiDB, which is a database of orthologous proteins, in plants, that correlates three major databases, OrthoDB, UniProt and RefSeq.  ...  KusakiDB could be a new approach to reduce error propagation of functional annotation in plant species.  ...  Reference sequence (RefSeq) database at NCBI: current status, 27 taxonomic expansion, and functional annotation. Nucleic Acids Res 2016;44(D1):D733-745. 28 Schnoes, A.M., et al.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.11.09.373753">doi:10.1101/2020.11.09.373753</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hy23t4jeu5aornjnhofz7vyv7u">fatcat:hy23t4jeu5aornjnhofz7vyv7u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210427085054/https://www.biorxiv.org/content/biorxiv/early/2020/11/10/2020.11.09.373753.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ee/df/eedf7f4b5d9a9f3e8d7203f68b7ac95f3949cf8d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.11.09.373753"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

The Universal Protein Resource (UniProt): an expanding universe of protein information

C. H. Wu
<span title="2006-01-01">2006</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The extensive cross-references, functional and feature annotations and literaturebased evidence attribution enable scientists to analyse proteins and query across databases.  ...  The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics.  ...  UniProtKB/Swiss-Prot activities at the SIB are supported by the Swiss Federal Government through the Federal Office of Education and Science.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkj161">doi:10.1093/nar/gkj161</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16381842">pmid:16381842</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1347523/">pmcid:PMC1347523</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6xrpacost5entptndstyr7gnry">fatcat:6xrpacost5entptndstyr7gnry</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170715110006/https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/nar/34/suppl_1/10.1093/nar/gkj161/2/gkj161.pdf?Expires=1500210005&amp;Signature=YytKGC6OkfOsuiUxqcOavAIrcLLTMmBd405tFBPtiN03Dhu-1hsZUoDOGRpAIZwpGeid0lFMztjshJgtO9DftkRKss8FIcl52BVpIJ1bFQ4hgxd92uph0JNaF~nwxSHyin6zbHjRwkZ-GX-GG0zkZdCVd7gasORD1aAMy6UAcjHSwXlsA~jHuamAPInk75EAPksyoWnW85j6xkd2MOGDRkgD53aks3CyfBQvP~6bFESi0ez7RblcziEB54zHfz7xlOk7DO-UdPt02XybT7mI9tQuJLsgPlZhUD9DLCzbJwHNnzPUYqNcUK3MSGqfJuqRf353kiv~~N~wuvN1pJi2Hw__&amp;Key-Pair-Id=APKAIUCZBIA4LVPAVW3Q" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fb/86/fb86a997ddc702a2924ffbc473bc9ed27c57566a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkj161"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347523" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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