RefSeq[Title] OR RefSeq[Abstract] - PMC

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Select item 105031981.

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 107679262.

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 101341973.

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

PMCID:: PMC10134197

Article PDF–3.6M

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 45023235.

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

Adam Frankish, Barbara Uszczynska, Graham RS Ritchie, Jose M Gonzalez, Dmitri Pervouchine, Robert Petryszak, Jonathan M Mudge, Nuno Fonseca, Alvis Brazma, Roderic Guigo, Jennifer Harrow

BMC Genomics. 2015; 16(Suppl 8): S2. Published online 2015 Jun 18. doi: 10.1186/1471-2164-16-S8-S2

PMCID:: PMC4502323

Article PDF–1001K

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

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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 1023938.

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 297879.

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 455193910.

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

Bhanu Rajput, Terence D. Murphy, Kim D. Pruitt

Nucleic Acids Res. 2015 Sep 3; 43(15): 7270–7279. Published online 2015 Jul 13. doi: 10.1093/nar/gkv713

PMCID:: PMC4551939

Article PDF–2.7M

Select item 388288911.

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 470284912.

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 620664013.

RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification

Daniel J. Nasko, Sergey Koren, Adam M. Phillippy, Todd J. Treangen

Genome Biol. 2018; 19: 165. Published online 2018 Oct 30. doi: 10.1186/s13059-018-1554-6

PMCID:: PMC6206640

Article PDF–1.0M

Select item 396503814.

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 418904415.

Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names

Jens H. Kuhn, Kristian G. Andersen, Yīmíng Bào, Sina Bavari, Stephan Becker, Richard S. Bennett, Nicholas H. Bergman, Olga Blinkova, Steven Bradfute, J. Rodney Brister, Alexander Bukreyev, Kartik Chandran, Alexander A. Chepurnov, Robert A. Davey, Ralf G. Dietzgen, Norman A. Doggett, Olga Dolnik, John M. Dye, Sven Enterlein, Paul W. Fenimore, Pierre Formenty, Alexander N. Freiberg, Robert F. Garry, Nicole L. Garza, Stephen K. Gire, Jean-Paul Gonzalez, Anthony Griffiths, Christian T. Happi, Lisa E. Hensley, Andrew S. Herbert, Michael C. Hevey, Thomas Hoenen, Anna N. Honko, Georgy M. Ignatyev, Peter B. Jahrling, Joshua C. Johnson, Karl M. Johnson, Jason Kindrachuk, Hans-Dieter Klenk, Gary Kobinger, Tadeusz J. Kochel, Matthew G. Lackemeyer, Daniel F. Lackner, Eric M. Leroy, Mark S. Lever, Elke Mühlberger, Sergey V. Netesov, Gene G. Olinger, Sunday A. Omilabu, Gustavo Palacios, Rekha G. Panchal, Daniel J. Park, Jean L. Patterson, Janusz T. Paweska, Clarence J. Peters, James Pettitt, Louise Pitt, Sheli R. Radoshitzky, Elena I. Ryabchikova, Erica Ollmann Saphire, Pardis C. Sabeti, Rachel Sealfon, Aleksandr M. Shestopalov, Sophie J. Smither, Nancy J. Sullivan, Robert Swanepoel, Ayato Takada, Jonathan S. Towner, Guido van der Groen, Viktor E. Volchkov, Valentina A. Volchkova, Victoria Wahl-Jensen, Travis K. Warren, Kelly L. Warfield, Manfred Weidmann, Stuart T. Nichol

Viruses. 2014 Sep; 6(9): 3663–3682. Published online 2014 Sep 26. doi: 10.3390/v6093663