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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  
mammalian RefSeq genomes.  ...  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 thank the numerous individual scientists who have contacted us over the years to suggest an improvement. We sincerely value your input to help improve the RefSeq database content.  ... 
doi:10.1093/nar/gkt1114 pmid:24259432 pmcid:PMC3965018 fatcat:wid54lruqrdzndb4oghwltdrqa

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)
2015 Mammalian Genome  
Complete and accurate annotation of the mouse genome is critical to the advancement of research conducted on this important model organism.  ...  We also thank the numerous individual scientists who have contacted us over the years to suggest an improvement. We sincerely value your input to help improve the RefSeq database content.  ...  More detailed information on NCBI RefSeq transcript and protein data for each gene is also available in the 'NCBI Reference Sequences (RefSeq)' section of the Gene page.  ... 
doi:10.1007/s00335-015-9585-8 pmid:26215545 pmcid:PMC4602073 fatcat:h7gzfdaghzeith7en6ejocoksi

RefSeq curation and annotation of stop codon recoding in vertebrates

Bhanu Rajput, Kim D Pruitt, Terence D Murphy
2018 Nucleic Acids Research  
Gene annotations were curated in nine vertebrate model organisms and integrated into NCBI's Reference Sequence (RefSeq) dataset, resulting in 247 selenoprotein genes encoding 322 selenoproteins, and 93  ...  ACKNOWLEDGEMENTS We would like to acknowledge RefSeq curators Catherine Farrell and David Webb, and developers Vamsi Kodali and Alexander Souvorov for helpful consults.  ...  in NCBI's Reference Sequence (RefSeq) database (26) .  ... 
doi:10.1093/nar/gky1234 pmid:30535227 pmcid:PMC6344875 fatcat:7uo7isrv7rfnji4nwlwhhrspme

Comparison of RefSeq protein-coding regions in human and vertebrate genomes

Jessica H Fong, Terence D Murphy, Kim D Pruitt
2013 BMC Genomics  
Results are available on the RefSeq FTP site [ftp://ftp.ncbi.nlm.nih.gov/refseq/supplemental/ProtCore/SM1.txt].  ...  Results: We assessed an ortholog dataset that includes 34 annotated vertebrate RefSeq genomes including human.  ...  splicing will be an interesting addition to RefSeq records.  ... 
doi:10.1186/1471-2164-14-654 pmid:24063302 pmcid:PMC3882889 fatcat:4dtx2aqljjctle2rzc55bayx6m

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  
The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of genomic, transcript and protein sequence records.  ...  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  ...  If a question arises, review of evidence from the stakeholder, the literature and sequence evidence may result in an update to a RefSeqGene record, revision of the reference transcripts and proteins annotated  ... 
doi:10.1093/nar/gkr1079 pmid:22121212 pmcid:PMC3245008 fatcat:n2exzcnlwbfi7ef24fcdeyuaca

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

K. D. Pruitt
2004 Nucleic Acids Research  
The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) provides a non-redundant collection of sequences representing genomic  ...  Sequences are annotated to include coding regions, conserved domains, variation, references, names, database cross-references, and other features using a combined approach of collaboration and other input  ...  Additional features including Enzyme Commission (EC) numbers, other landmark regions of the protein sequence and references may be added by curation either by an external collaborator or by NCBI staff.  ... 
doi:10.1093/nar/gki025 pmid:15608248 pmcid:PMC539979 fatcat:gneoq6nakbeptfwoymdt4kfj4e

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.  ...  The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence  ...  (xi) Indel: transcript has insertions or deletions versus the reference genome sequence. (xii) Mismatches: transcript has one or more mismatches versus the reference genome sequence.  ... 
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  
a standard set of stable, non-redundant reference sequences.  ...  The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature.  ...  thank the scientific community for constructive feedback, suggestions, error reports, and collaborations over the last 15 years that have contributed toward the quality and accuracy of the represented sequence  ... 
doi:10.1093/nar/gkv1189 pmid:26553804 pmcid:PMC4702849 fatcat:2bm7d5coyvfotaj23hnj3mce6m

RefSeq curation and annotation of antizyme and antizyme inhibitor genes in vertebrates

Bhanu Rajput, Terence D. Murphy, Kim D. Pruitt
2015 Nucleic Acids Research  
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  ... 
doi:10.1093/nar/gkv713 pmid:26170238 pmcid:PMC4551939 fatcat:hou3eb5l6rdmxj4ptfxwkurvu4

RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse

Catherine M Farrell, Tamara Goldfarb, Sanjida H Rangwala, Alexander Astashyn, Olga D Ermolaeva, Vichet Hem, Kenneth S Katz, Vamsi K Kodali, Frank Ludwig, Craig L Wallin, Kim D Pruitt, Terence D Murphy
2021 biorxiv/medrxiv  
The curated dataset is comprised of richly annotated sequence records, descriptive records in the NCBI Gene database, reference genome feature annotation, and activity-based interactions between nongenic  ...  RefSeqFEs thus provide an alternative and complementary resource for experimentally assayed functional elements, with future dataset growth expected.  ...  and tools, full indexing and versioning of sequence records, and the ability to update records and genome annotation, including on new genome assemblies.  ... 
doi:10.1101/gr.275819.121 pmid:34876495 pmcid:PMC8744684 fatcat:dichersxxfcdfijtp33emabx3u

NCBI Reference Sequences: current status, policy and new initiatives

K. D. Pruitt, T. Tatusova, W. Klimke, D. R. Maglott
2009 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 and represent a current description of the sequence, the gene and sequence features.  ...  RefSeq chromosome sequences are also used, but the coordinate system is unappealingly large and, perhaps more importantly, not as stable because the human reference sequence continues to be updated.  ... 
doi:10.1093/nar/gkn721 pmid:18927115 pmcid:PMC2686572 fatcat:77xptvs54fghxb3dur3ykwycgq

The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context

A. Ruepp
2006 Nucleic Acids Research  
Manual annotation concentrates on proteins which are found to interact physically with other proteins.  ...  Accordingly, manually curated information from a 20 protein-protein interaction database (MPPI) and a database of mammalian protein complexes is interconnected with MfunGD.  ...  In addition, MfunGD 35 contains information about literature that was used for manual annotation as well as protein ID, FunCat annotation, comments, update information and cross-references to RefSeq, UniProt  ... 
doi:10.1093/nar/gkj074 pmid:16381934 pmcid:PMC1347437 fatcat:ngwijbsxqzb53crfahoi4ppjhy

CRONOS: the cross-reference navigation server

Brigitte Waegele, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Corinna Montrone, H.-Werner Mewes, Andreas Ruepp
2008 Computer applications in the biosciences : CABIOS  
Sequence similarity analysis of the mapped entries shows that the cross-references are highly accurate.  ...  To overcome this, we developed CRONOS, a cross-reference server that contains entries from five mammalian organisms presented by major gene and protein information resources.  ...  METHODS Generation of cross-references Building of the cross-references is performed with data from five mammalian organisms (human, mouse, rat, cow and dog) using UniProt, RefSeq and Ensembl as primary  ... 
doi:10.1093/bioinformatics/btn590 pmid:19010804 pmcid:PMC2638938 fatcat:asaoknrz6nc2ndfcsltmyv7isi

Assembly: a resource for assembled genomes at NCBI

Paul A. Kitts, Deanna M. Church, Françoise Thibaud-Nissen, Jinna Choi, Vichet Hem, Victor Sapojnikov, Robert G. Smith, Tatiana Tatusova, Charlie Xiang, Andrey Zherikov, Michael DiCuccio, Terence D. Murphy (+2 others)
2015 Nucleic Acids Research  
The database provides an assembly accession and version to unambiguously identify the set of sequences that make up a particular version of an assembly, and tracks changes to updated genome assemblies.  ...  The Assembly database also tracks the relationship between an assembly submitted to the International Nucleotide Sequence Database Consortium (INSDC) and the assembly represented in the NCBI RefSeq project  ...  We are grateful to our project managers, Anatoly Mnev and Robert Cohen, for keeping both projects on track and moving forward.  ... 
doi:10.1093/nar/gkv1226 pmid:26578580 pmcid:PMC4702866 fatcat:2snbt2r7jjdczkqiyjihn5jpxi

The completion of the Mammalian Gene Collection (MGC)

G. Temple, D. S. Gerhard, R. Rasooly, E. A. Feingold, P. J. Good, C. Robinson, A. Mandich, J. G. Derge, J. Lewis, D. Shoaf, F. S. Collins, W. Jang (+115 others)
2009 Genome Research  
The Mammalian Gene Collection Program was an NIH interinstitute effort that received financial and scientific support from 19 institutes within the NIH.  ...  A complete list of these institutes is provided on the MGC website. Greg Schuler and Karl Sirotkin provided valuable bioinformatics advice to MGC.  ...  Resource The completion of the Mammalian Gene Collection (MGC) The MGC Project Team 1 Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence  ... 
doi:10.1101/gr.095976.109 pmid:19767417 pmcid:PMC2792178 fatcat:bbfbbxrrirc6zlmjrd6a4gqivy
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