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2. GenBank 2024 Update

Author

Sayers, Eric W, primary, Cavanaugh, Mark, additional, Clark, Karen, additional, Pruitt, Kim D, additional, Sherry, Stephen T, additional, Yankie, Linda, additional, and Karsch-Mizrachi, Ilene, additional

Published
2023
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4. GenBank 2024 Update.

Author

Sayers, Eric W, Cavanaugh, Mark, Clark, Karen, Pruitt, Kim D, Sherry, Stephen T, Yankie, Linda, and Karsch-Mizrachi, Ilene

Published
2024
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5. GenBank 2023 update

Author

Sayers, Eric W, primary, Cavanaugh, Mark, additional, Clark, Karen, additional, Pruitt, Kim D, additional, Sherry, Stephen T, additional, Yankie, Linda, additional, and Karsch-Mizrachi, Ilene, additional

Published
2022
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6. Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank

Author

Underwood, Beverly A, primary, Yankie, Linda, additional, Nawrocki, Eric P, additional, Palanigobu, Vasuki, additional, Gotvyanskyy, Sergiy, additional, Calhoun, Vincent C, additional, Kornbluh, Michael, additional, Smith, Thomas G, additional, Fleischmann, Lydia, additional, Sinyakov, Denis, additional, Bollin, Colleen J, additional, and Karsch-Mizrachi, Ilene, additional

Published
2022
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7. VADR: validation and annotation of virus sequence submissions to GenBank

Author

Massachusetts Institute of Technology. Department of Biology, Schäffer, Alejandro A., Hatcher, Eneida L., Yankie, Linda, Shonkwiler, Lara, Brister, J. Rodney, Karsch-Mizrachi, Ilene, Nawrocki, Eric P., Massachusetts Institute of Technology. Department of Biology, Schäffer, Alejandro A., Hatcher, Eneida L., Yankie, Linda, Shonkwiler, Lara, Brister, J. Rodney, Karsch-Mizrachi, Ilene, and Nawrocki, Eric P.

Abstract

Background GenBank contains over 3 million viral sequences. The National Center for Biotechnology Information (NCBI) previously made available a tool for validating and annotating influenza virus sequences that is used to check submissions to GenBank. Before this project, there was no analogous tool in use for non-influenza viral sequence submissions. Results We developed a system called VADR (Viral Annotation DefineR) that validates and annotates viral sequences in GenBank submissions. The annotation system is based on the analysis of the input nucleotide sequence using models built from curated RefSeqs. Hidden Markov models are used to classify sequences by determining the RefSeq they are most similar to, and feature annotation from the RefSeq is mapped based on a nucleotide alignment of the full sequence to a covariance model. Predicted proteins encoded by the sequence are validated with nucleotide-to-protein alignments using BLAST. The system identifies 43 types of “alerts” that (unlike the previous BLAST-based system) provide deterministic and rigorous feedback to researchers who submit sequences with unexpected characteristics. VADR has been integrated into GenBank’s submission processing pipeline allowing for viral submissions passing all tests to be accepted and annotated automatically, without the need for any human (GenBank indexer) intervention. Unlike the previous submission-checking system, VADR is freely available (https://github.com/nawrockie/vadr) for local installation and use. VADR has been used for Norovirus submissions since May 2018 and for Dengue virus submissions since January 2019. Since March 2020, VADR has also been used to check SARS-CoV-2 sequence submissions. Other viruses with high numbers of submissions will be added incrementally. Conclusion VADR improves the speed with which non-flu virus submissions to GenBank can be checked and improves the content and quality of the GenBank annotations. The availability and portability of the soft

Published
2020

9. Determination of the nucleotide binding site within Clostridium symbiosum pyruvate phosphate dikinase by photoaffinity labeling, site-directed mutagenesis, and structural analysis

Author

McGuire, Marielena, Carroll, Lawrence J., Yankie, Linda, Thrall, Sara H., Dunaway-Mariano, Debra, Herzberg, Osnat, Jayaram, Beby, and Haley, Boyd H.

Subjects
Clostridium -- Research, Binding sites (Biochemistry) -- Research, Microbial enzymes -- Physiological aspects, Biological sciences, Chemistry
Abstract

Photoaffinity labeling, site-directed mutagenesis and structural analysis of pyruvate phosphate dikinase from Clostridium symbiosum reveals that the nucleotide binding site is present in the N-terminal. X-ray crystal structure studies indicates that the enzyme folds into N-terminal, central and C-terminal regions. ATP binds in a crevice formed by subdomains one and three in a manner similar to ADP binding in D-alanine-D-alanine-ligase.

Published
1996

10. Location of the catalytic site for phosphoenolpyruvate formation within the primary structure of Clostridium symbiosum pyruvate phosphate dikinase. 1. Identification of an essential cysteine by chemical modification with (1-14C)bromopyruvate and site-directed mutagenesis

Author

Xu, Yuan, Yankie, Linda, Shen, Li, Jung, Young-Shik, Mariano, Patrick S., Dunaway-Mariano, Debra, and Martin, Brian M.

Subjects
Clostridium -- Research, Microbial enzymes -- Analysis, Binding sites (Biochemistry) -- Analysis, Biological sciences, Chemistry
Abstract

Reduction of Clostridium symbiosum pyruvate phosphate dikinase (PPDK) treated with the affinity label (1-14C)bromopyruvate by NaBH4, followed by proteolysis with trypsin reveal that the alkylation site in the enzyme is Cys 831. Kinetic analysis of the C831A PPDK mutant, generated by substituting Ala for Cys 831, reveals that the both mutant and wild-type PPDK exhibit equal efficiency in catalyzing nucleotide partial reduction, while the mutant fails to catalyze the pyruvate partial reduction. Cys 831 is essential for phosphoenol-pyruvate/pyruvate binding and or catalysis.

Published
1995

11. Location of the catalytic site for phosphoenolpyruvate formation within the primary structure of Clostridium symbiosum pyruvate phosphate dikinase. 2. Site-directed mutagenesis of an essential arginine contained within an apparent P-loop

Author

Yankie, Linda, Xu, Yuan, and Dunaway-Mariano, Debra

Subjects
Clostridium -- Research, Microbial enzymes -- Analysis, Binding sites (Biochemistry) -- Analysis, Biological sciences, Chemistry
Abstract

Examination of the catalytic properties of two Clostridium symbiosum pyruvate phosphate dikinase (PPDK) site-directed mutants, one having Leu 561 for Arg 561 and other having Lys 561 for Arg 561, reveals that both mutants fail to catalyze the full PPDK reaction and phosphoenol pyruvate (PEP) pyruvate partial reaction. The active site of the PEP/pyruvate partial reaction has Arg 561 and a Gly-rich conserved stretch of sequence spanning positions 553-563, which has a phosphoryl group binding unit in the 35 kDa domains.

Published
1995

12. NCBI will no longer make taxonomy identifiers for individual influenza strains on January 15, 2018

Author

Hatcher, Eneida, primary, Bao, Yiming, additional, Amedeo, Paolo, additional, Blinkova, Olga, additional, Cochrane, Guy, additional, Fedorova, Nadia, additional, Gruner, William, additional, Leipe, Detlef, additional, Nakamura, Yasukazu, additional, Ostapchuk, Yuri, additional, Palanigobu, Vasuki, additional, Sanders, Robert, additional, Schoch, Conrad, additional, Smith, Catherine, additional, Wentworth, David, additional, Yankie, Linda, additional, Zhdanov, Sergey, additional, Karsch-Mizrachi, Ilene, additional, and Brister, J. Rodney, additional

Published
2017
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13. The completion of the Mammalian Gene Collection (MGC)

Author

Temple, Gary, Gerhard, Daniela, Rasooly, S. Rebekah, Feingold, Elise A., Good, Peter J., Robinson, Cristen, Mandich, Allison, Derge, Jeffrey G., Lewis, Jeanne, Shoaf, Debonny, Collins, Francis S., Wonhee Jang, Wagner, Lukas, Shenmen, Carolyn M., Misquitta, Leonie, Schaefer, Carl F., Buetow, Kenneth H., Bonner, Tom I., Yankie, Linda, Ward, Ming, Phan, Lon, Astashyn, Alex, Brown, Garth, Farrell, Catherine, Hart, Jennifer, Landrum, Melissa, Maidak, Bonnie L., Murphy, Michael, Murphy, Terence, Rajput, Bhanu, Riddick, Lillian, Webb, David, Weber, Janet, Wu, Wendy, Pruitt, Kim D., Maglott, Donna, Siepel, Adam, Brejova, Brona, Diekhans, Mark, Harte, Rachel, Baertsch, Robert, Kent, Jim, Haussler, David, Brent, Michael, Langton, Laura, Comstock, Charles L.G., Stevens, Michael, Chaochun Wei, van Baren, Marijke J., Salehi-Ashtiani, Kourosh, Murray, Ryan R., Ghamsari, Lila, Mello, Elizabeth, Chenwei Lin, Pennacchio, Christa, Schreiber, Kirsten, Shapiro, Nicole, Marsh, Amber, Pardes, Elizabeth, Moore, Troy, Lebeau, Anita, Muratet, Mike, Simmons, Blake, Kloske, David, Sieja, Stephanie, Hudson, James, Sethupathy, Praveen, Brownstein, Michael, Bhat, Narayan, Lazar, Joseph, Jacob, Howard, Gruber, Chris E., Smith, Mark R., McPherson, John, Garcia, Angela M., Gunaratne, Preethi H., Jiaqian Wu, Muzny, Donna, Gibbs, Richard A., Young, Alice C., Bouffard, Gerard G., Blakesley, Robert W., Mullikin, Jim, Green, Eric D., Dickson, Mark C., Rodriguez, Alex C., Grimwood, Jane, Schmutz, Jeremy, Myers, Richard M., Hirst, Martin, Zeng, Thomas, Kane Tse, Moksa, Michelle, Deng, Merinda, Ma, Kevin, Mah, Diana, Pang, Johnson, Taylor, Greg, Chuah, Eric, Deng, Athena, Fichter, Keith, Go, Anne, Lee, Stephanie, Jing Wang, Griffith, Malachi, Morin, Ryan, Moore, Richard A., Mayo, Michael, Munro, Sarah, Wagner, Susan, Jones, Steven J.M., Holt, Robert A., Marra, Marco A., Sun Lu, Shuwei Yang, Hartigan, James, Graf, Marcus, Wagner, Ralf, Letovksy, Stanley, Pulido, Jacqueline C., Robison, Keith, Esposito, Dominic, Hartley, James, Wall, Vanessa E., Hopkins, Ralph F., Osamu Ohara, and Wiemann, Stefan

Subjects
DNA synthesis -- Research, Mammals -- Genetic aspects, Nucleotide sequencing -- Evaluation, Genetic transcription -- Research, Health
Published
2009

14. Influenza sequence validation and annotation using VADR.

Author

Calhoun VC, Hatcher EL, Yankie L, and Nawrocki EP

Subjects
Humans, Orthomyxoviridae genetics, Influenza, Human virology, Influenza, Human genetics, Databases, Nucleic Acid, Molecular Sequence Annotation methods, Software
Abstract

Tens of thousands of influenza sequences are deposited into the GenBank database each year. The software tool FLu ANnotation tool (FLAN) has been used by GenBank since 2007 to validate and annotate incoming influenza sequence submissions and has been publicly available as a webserver but not as a standalone tool. Viral Annotation DefineR (VADR) is a general sequence validation and annotation software package used by GenBank for norovirus, dengue virus and SARS-CoV-2 virus sequence processing that is available as a standalone tool. We have created VADR influenza models based on the FLAN reference sequences and adapted VADR to accurately annotate influenza sequences. VADR and FLAN show consistent results on the vast majority of influenza sequences, and when they disagree, VADR is usually correct. VADR can also accurately process influenza D sequences as well as influenza A H17, H18, H19, N10 and N11 subtype sequences, which FLAN cannot. VADR 1.6.3 and the associated influenza models are now freely available for users to download and use. Database URL: https://bitbucket.org/nawrockie/vadr-models-flu., (Published by Oxford University Press 2024. This work is written by (a) US Government employee(s) and is in the public domain in the US.)

Published
2024
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