RefSeq[Title] OR RefSeq[Abstract] - PMC

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Select item 107679261.

RefSeq and the prokaryotic genome annotation pipeline in the age of metagenomes

Daniel H Haft, Azat Badretdin, George Coulouris, Michael DiCuccio, A Scott Durkin, Eric Jovenitti, Wenjun Li, Megdelawit Mersha, Kathleen R O’Neill, Joel Virothaisakun, Françoise Thibaud-Nissen

Nucleic Acids Res. 2024 Jan 5; 52(D1): D762–D769. Published online 2023 Nov 14. doi: 10.1093/nar/gkad988

PMCID:: PMC10767926

Article PDF–1.4M

Select item 105031982.

Lifting of the 1,000 wheat exome project SNPs from Triticum aestivum cv. Chinese Spring assembly RefSeq v1.0 to RefSeq v2.1

Akshaya Vasudevan, Sylvie Cloutier

BMC Res Notes. 2023; 16: 220. Published online 2023 Sep 14. doi: 10.1186/s13104-023-06496-8

PMCID:: PMC10503198

Article PDF–2.0M

Select item 117016643.

NCBI RefSeq: reference sequence standards through 25 years of curation and annotation

Tamara Goldfarb, Vamsi K Kodali, Shashikant Pujar, Vyacheslav Brover, Barbara Robbertse, Catherine M Farrell, Dong-Ha Oh, Alexander Astashyn, Olga Ermolaeva, Diana Haddad, Wratko Hlavina, Jinna Hoffman, John D Jackson, Vinita S Joardar, David Kristensen, Patrick Masterson, Kelly M McGarvey, Richard McVeigh, Eyal Mozes, Michael R Murphy, Susan S Schafer, Alexander Souvorov, Brett Spurrier, Pooja K Strope, Hanzhen Sun, Anjana R Vatsan, Craig Wallin, David Webb, J Rodney Brister, Eneida Hatcher, Avi Kimchi, William Klimke, Aron Marchler-Bauer, Kim D Pruitt, Françoise Thibaud-Nissen, Terence D Murphy

Nucleic Acids Res. 2025 Jan 6; 53(D1): D243–D257. Published online 2024 Nov 11. doi: 10.1093/nar/gkae1038

PMCID:: PMC11701664

Article PDF–1.7M

Select item 37122164.

EcoGene-RefSeq: EcoGene tools applied to the RefSeq prokaryotic genomes

Jindan Zhou, Andrew J. Richardson, Kenneth E. Rudd

Bioinformatics. 2013 Aug 1; 29(15): 1917–1918. Published online 2013 Jun 4. doi: 10.1093/bioinformatics/btt302

PMCID:: PMC3712216

Article PDF–113K

Select item 101341975.

Revisiting and corrections to the annotated SRSF3 (SRp20) gene structure and RefSeq sequences from the human and mouse genomes

Lulu Yu, Vladimir Majerciak, Rong Jia, Zhi-Ming Zheng

Cell Insight. 2023 Apr; 2(2): 100089. Published online 2023 Feb 26. doi: 10.1016/j.cellin.2023.100089

Correction in:: Cell Insight. 2025 Apr; 4(2): 100225.

PMCID:: PMC10134197

Article PDF–3.6M

Select item 77790086.

RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation

Wenjun Li, Kathleen R O’Neill, Daniel H Haft, Michael DiCuccio, Vyacheslav Chetvernin, Azat Badretdin, George Coulouris, Farideh Chitsaz, Myra K Derbyshire, A Scott Durkin, Noreen R Gonzales, Marc Gwadz, Christopher J Lanczycki, James S Song, Narmada Thanki, Jiyao Wang, Roxanne A Yamashita, Mingzhang Yang, Chanjuan Zheng, Aron Marchler-Bauer, Françoise Thibaud-Nissen

Nucleic Acids Res. 2021 Jan 8; 49(D1): D1020–D1028. Published online 2020 Dec 3. doi: 10.1093/nar/gkaa1105

PMCID:: PMC7779008

Article PDF–1.1M

Select item 57533317.

RefSeq: an update on prokaryotic genome annotation and curation

Daniel H Haft, Michael DiCuccio, Azat Badretdin, Vyacheslav Brover, Vyacheslav Chetvernin, Kathleen O’Neill, Wenjun Li, Farideh Chitsaz, Myra K Derbyshire, Noreen R Gonzales, Marc Gwadz, Fu Lu, Gabriele H Marchler, James S Song, Narmada Thanki, Roxanne A Yamashita, Chanjuan Zheng, Françoise Thibaud-Nissen, Lewis Y Geer, Aron Marchler-Bauer, Kim D Pruitt

Nucleic Acids Res. 2018 Jan 4; 46(Database issue): D851–D860. Published online 2017 Nov 3. doi: 10.1093/nar/gkx1068

PMCID:: PMC5753331

Article PDF–225K

Select item 113683858.

refseqR: an R package for common computational operations with records on RefSeq collection

Jose V Die

Bioinform Adv. 2024; 4(1): vbae122. Published online 2024 Aug 21. doi: 10.1093/bioadv/vbae122

PMCID:: PMC11368385

Article PDF–380K

Select item 17167189.

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

Kim D. Pruitt, Tatiana Tatusova, Donna R. Maglott

Nucleic Acids Res. 2007 Jan; 35(Database issue): D61–D65. Published online 2006 Nov 27. doi: 10.1093/nar/gkl842

PMCID:: PMC1716718

Article PDF–241K

Select item 53997910.

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

Kim D. Pruitt, Tatiana Tatusova, Donna R. Maglott

Nucleic Acids Res. 2005 Jan 1; 33(Database Issue): D501–D504. Published online 2004 Dec 17. doi: 10.1093/nar/gki025

PMCID:: PMC539979

Article PDF–62K

Select item 2978711.

RefSeq and LocusLink: NCBI gene-centered resources

Kim D. Pruitt, Donna R. Maglott

Nucleic Acids Res. 2001 Jan 1; 29(1): 137–140. doi: 10.1093/nar/29.1.137

PMCID:: PMC29787

Article PDF–108K

Select item 438390312.

Update on RefSeq microbial genomes resources

Tatiana Tatusova, Stacy Ciufo, Scott Federhen, Boris Fedorov, Richard McVeigh, Kathleen O'Neill, Igor Tolstoy, Leonid Zaslavsky

Nucleic Acids Res. 2015 Jan 28; 43(Database issue): D599–D605. Published online 2014 Dec 15. doi: 10.1093/nar/gku1062

PMCID:: PMC4383903

Article PDF–1.2M

Select item 10239313.

NCBI’s LocusLink and RefSeq

Donna R. Maglott, Kenneth S. Katz, Hugues Sicotte, Kim D. Pruitt

Nucleic Acids Res. 2000 Jan 1; 28(1): 126–128. doi: 10.1093/nar/28.1.126

PMCID:: PMC102393

Article PDF–77K

Select item 388288914.

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

Jessica H Fong, Terence D Murphy, Kim D Pruitt

BMC Genomics. 2013; 14: 654. Published online 2013 Sep 25. doi: 10.1186/1471-2164-14-654

PMCID:: PMC3882889

Article PDF–1.6M

Select item 324500815.

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

Kim D. Pruitt, Tatiana Tatusova, Garth R. Brown, Donna R. Maglott

Nucleic Acids Res. 2012 Jan; 40(Database issue): D130–D135. Published online 2011 Nov 24. doi: 10.1093/nar/gkr1079

PMCID:: PMC3245008

Article PDF–1.7M

Select item 470284916.

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, Yiming Bao, Olga Blinkova, Vyacheslav Brover, Vyacheslav Chetvernin, Jinna Choi, Eric Cox, Olga Ermolaeva, Catherine M. Farrell, Tamara Goldfarb, Tripti Gupta, Daniel Haft, Eneida Hatcher, Wratko Hlavina, Vinita S. Joardar, Vamsi K. Kodali, Wenjun Li, Donna Maglott, Patrick Masterson, Kelly M. McGarvey, Michael R. Murphy, Kathleen O'Neill, Shashikant Pujar, Sanjida H. Rangwala, Daniel Rausch, Lillian D. Riddick, Conrad Schoch, Andrei Shkeda, Susan S. Storz, Hanzhen Sun, Francoise Thibaud-Nissen, Igor Tolstoy, Raymond E. Tully, Anjana R. Vatsan, Craig Wallin, David Webb, Wendy Wu, Melissa J. Landrum, Avi Kimchi, Tatiana Tatusova, Michael DiCuccio, Paul Kitts, Terence D. Murphy, Kim D. Pruitt

Nucleic Acids Res. 2016 Jan 4; 44(Database issue): D733–D745. Published online 2015 Nov 8. doi: 10.1093/nar/gkv1189

PMCID:: PMC4702849

Article PDF–168K

Select item 760430217.

The Most Frequently Used Sequencing Technologies and Assembly Methods in Different Time Segments of the Bacterial Surveillance and RefSeq Genome Databases

Bo Segerman

Front Cell Infect Microbiol. 2020; 10: 527102. Published online 2020 Oct 19. doi: 10.3389/fcimb.2020.527102

PMCID:: PMC7604302

Article PDF–1.1M

Select item 396503818.

RefSeq microbial genomes database: new representation and annotation strategy

Tatiana Tatusova, Stacy Ciufo, Boris Fedorov, Kathleen O’Neill, Igor Tolstoy

Nucleic Acids Res. 2014 Jan 1; 42(Database issue): D553–D559. Published online 2013 Dec 7. doi: 10.1093/nar/gkt1274

Correction in:: Nucleic Acids Res. 2015 Apr 20; 43(7): 3872.

PMCID:: PMC3965038

Article PDF–6.3M

Select item 460207319.

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, Lillian D. Riddick, David Webb, Mathew W. Wright, Terence D. Murphy, Kim D. Pruitt

Mamm Genome. 2015; 26(9-10): 379–390. Published online 2015 Jul 28. doi: 10.1007/s00335-015-9585-8

PMCID:: PMC4602073

Article PDF–1.7M

Select item 334602120.

Automation of a primer design and evaluation pipeline for subsequent sequencing of the coding regions of all human Refseq genes

Daniel Lai, Donald R Love

Bioinformation. 2012; 8(8): 365–368. Published online 2012 Apr 30. doi: 10.6026/97320630008365

PMCID:: PMC3346021

Article PDF–313K

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