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4. Database resources of the National Center for Biotechnology Information

Author

Sayers, Eric W., Barrett, Tanya, Benson, Dennis A., Bolton, Evan, Bryant, Stephen H., Canese, Kathi, Chetvernin, Vyacheslav, Church, Deanna M., DiCuccio, Michael, Federhen, Scott, Feolo, Michael, Fingerman, Ian M., Geer, Lewis Y., Helmberg, Wolfgang, Kapustin, Yuri, Krasnov, Sergey, Landsman, David, Lipman, David J., Lu, Zhiyong, Madden, Thomas L., Madej, Tom, Maglott, Donna R., Marchler-Bauer, Aron, Miller, Vadim, Karsch-Mizrachi, Ilene, Ostell, James, Panchenko, Anna, Phan, Lon, Pruitt, Kim D., Schuler, Gregory D., Sequeira, Edwin, Sherry, Stephen T., Shumway, Martin, Sirotkin, Karl, Slotta, Douglas, Souvorov, Alexandre, Starchenko, Grigory, Tatusova, Tatiana A., Wagner, Lukas, Wang, Yanli, Wilbur, W. John, Yaschenko, Eugene, and Ye, Jian

Published
2012
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5. Database resources of the National Center for Biotechnology Information

Author

Sayers, Eric W., Barrett, Tanya, Benson, Dennis A., Bolton, Evan, Bryant, Stephen H., Canese, Kathi, Chetvernin, Vyacheslav, Church, Deanna M., DiCuccio, Michael, Federhen, Scott, Feolo, Michael, Fingerman, Ian M., Geer, Lewis Y., Helmberg, Wolfgang, Kapustin, Yuri, Landsman, David, Lipman, David J., Lu, Zhiyong, Madden, Thomas L., Madej, Tom, Maglott, Donna R., Marchler-Bauer, Aron, Miller, Vadim, Mizrachi, Ilene, Ostell, James, Panchenko, Anna, Phan, Lon, Pruitt, Kim D., Schuler, Gregory D., Sequeira, Edwin, Sherry, Stephen T., Shumway, Martin, Sirotkin, Karl, Slotta, Douglas, Souvorov, Alexandre, Starchenko, Grigory, Tatusova, Tatiana A., Wagner, Lukas, Wang, Yanli, Wilbur, W. John, Yaschenko, Eugene, and Ye, Jian

Published
2011
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6. Database resources of the National Center for Biotechnology Information

Author

Sayers, Eric W., Barrett, Tanya, Benson, Dennis A., Bolton, Evan, Bryant, Stephen H., Canese, Kathi, Chetvernin, Vyacheslav, Church, Deanna M., DiCuccio, Michael, Federhen, Scott, Feolo, Michael, Geer, Lewis Y., Helmberg, Wolfgang, Kapustin, Yuri, Landsman, David, Lipman, David J., Lu, Zhiyong, Madden, Thomas L., Madej, Tom, Maglott, Donna R., Marchler-Bauer, Aron, Miller, Vadim, Mizrachi, Ilene, Ostell, James, Panchenko, Anna, Pruitt, Kim D., Schuler, Gregory D., Sequeira, Edwin, Sherry, Stephen T., Shumway, Martin, Sirotkin, Karl, Slotta, Douglas, Souvorov, Alexandre, Starchenko, Grigory, Tatusova, Tatiana A., Wagner, Lukas, Wang, Yanli, John Wilbur, W., Yaschenko, Eugene, and Ye, Jian

Published
2010
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7. Database resources of the National Center for Biotechnology Information

Author

Sayers, Eric W., Barrett, Tanya, Benson, Dennis A., Bryant, Stephen H., Canese, Kathi, Chetvernin, Vyacheslav, Church, Deanna M., DiCuccio, Michael, Edgar, Ron, Federhen, Scott, Feolo, Michael, Geer, Lewis Y., Helmberg, Wolfgang, Kapustin, Yuri, Landsman, David, Lipman, David J., Madden, Thomas L., Maglott, Donna R., Miller, Vadim, Mizrachi, Ilene, Ostell, James, Pruitt, Kim D., Schuler, Gregory D., Sequeira, Edwin, Sherry, Stephen T., Shumway, Martin, Sirotkin, Karl, Souvorov, Alexandre, Starchenko, Grigory, Tatusova, Tatiana A., Wagner, Lukas, Yaschenko, Eugene, and Ye, Jian

Published
2009

8. Working together to put molecules on the map

Author

Field, Dawn, Morrison, Norman, Glöckner, Frank Oliver, Kottmann, Renzo, Cochrane, Guy, Vaughan, Robert, Garrity, George, Cole, Jim, Hirschman, Lynette, Schriml, Lynn, Mizrachi, Ilene, Federhen, Scott, Schindel, David, Miller, Scott, Hebert, Paul, Ratnasingham, Sujeevan, Hanner, Robert, Amaral-Zettler, Linda, Sogin, Mitchell, Ashburner, Michael, Lewis, Suzanna, and Smith, Barry

Published
2008
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9. Database resources of the National Center for Biotechnology Information

Author

Wheeler, David L., Barrett, Tanya, Benson, Dennis A., Bryant, Stephen H., Canese, Kathi, Chetvernin, Vyacheslav, Church, Deanna M., DiCuccio, Michael, Edgar, Ron, Federhen, Scott, Feolo, Michael, Geer, Lewis Y., Helmberg, Wolfgang, Kapustin, Yuri, Khovayko, Oleg, Landsman, David, Lipman, David J., Madden, Thomas L., Maglott, Donna R., Miller, Vadim, Ostell, James, Pruitt, Kim D., Schuler, Gregory D., Shumway, Martin, Sequeira, Edwin, Sherry, Steven T., Sirotkin, Karl, Souvorov, Alexandre, Starchenko, Grigory, Tatusov, Roman L., Tatusova, Tatiana A., Wagner, Lukas, and Yaschenko, Eugene

Published
2008

10. Database resources of the National Center for Biotechnology Information

Author

Wheeler, David L., Barrett, Tanya, Benson, Dennis A., Bryant, Stephen H., Canese, Kathi, Chetvernin, Vyacheslav, Church, Deanna M., DiCuccio, Michael, Edgar, Ron, Federhen, Scott, Geer, Lewis Y., Kapustin, Yuri, Khovayko, Oleg, Landsman, David, Lipman, David J., Madden, Thomas L., Maglott, Donna R., Ostell, James, Miller, Vadim, Pruitt, Kim D., Schuler, Gregory D., Sequeira, Edwin, Sherry, Steven T., Sirotkin, Karl, Souvorov, Alexandre, Starchenko, Grigory, Tatusov, Roman L., Tatusova, Tatiana A., Wagner, Lukas, and Yaschenko, Eugene

Published
2007

11. Database resources of the National Center for Biotechnology Information

Author

Wheeler, David L., Barrett, Tanya, Benson, Dennis A., Bryant, Stephen H., Canese, Kathi, Chetvernin, Vyacheslav, Church, Deanna M., DiCuccio, Michael, Edgar, Ron, Federhen, Scott, Geer, Lewis Y., Helmberg, Wolfgang, Kapustin, Yuri, Kenton, David L., Khovayko, Oleg, Lipman, David J., Madden, Thomas L., Maglott, Donna R., Ostell, James, Pruitt, Kim D., Schuler, Gregory D., Schriml, Lynn M., Sequeira, Edwin, Sherry, Stephen T., Sirotkin, Karl, Souvorov, Alexandre, Starchenko, Grigory, Suzek, Tugba O., Tatusov, Roman, Tatusova, Tatiana A., Wagner, Lukas, and Yaschenko, Eugene

Published
2006

12. Database resources of the National Center for Biotechnology Information

Author

Wheeler, David L., Barrett, Tanya, Benson, Dennis A., Bryant, Stephen H., Canese, Kathi, Church, Deanna M., DiCuccio, Michael, Edgar, Ron, Federhen, Scott, Helmberg, Wolfgang, Kenton, David L., Khovayko, Oleg, Lipman, David J., Madden, Thomas L., Maglott, Donna R., Ostell, James, Pontius, Joan U., Pruitt, Kim D., Schuler, Gregory D., Schriml, Lynn M., Sequeira, Edwin, Sherry, Steven T., Sirotkin, Karl, Starchenko, Grigory, Suzek, Tugba O., Tatusov, Roman, Tatusova, Tatiana A., Wagner, Lukas, and Yaschenko, Eugene

Published
2005

15. Meeting report: GenBank microbial genomic taxonomy workshop (12-13 May, 2015).

Author

Federhen, Scott, Rossello-Mora, Ramon, Klenk, Hans-Peter, Tindall, Brian, Konstantinidis, Konstantinos, Whitman, William, Brown, Daniel, Labeda, David, Ussery, David, Garrity, George, Colwell, Rita, Hasan, Nur, Graf, Joerg, Parte, Aidan, Yarza, Pablo, Goldberg, Brittany, Sichtig, Heike, Karsch-Mizrachi, Ilene, Clark, Karen, and McVeigh, Richard

Subjects
*MICROBIAL genomics, *GENE libraries, *CLASSIFICATION of microorganisms, *BACTERIAL communities, *BACTERIAL genomes
Abstract

Many genomes are incorrectly identified at GenBank. We developed a plan to find and correct misidentified genomes using genomic comparison statistics together with a scaffold of reliably identified genomes from type. A workshop was organized with broad representation from the bacterial taxonomic community to review the proposal, the GenBank Microbial Genomic Taxonomy Workshop, Bethesda MD, May 12-13, 2015. [ABSTRACT FROM AUTHOR]

Published
2016
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16. TAXONOMY OF SIMPLE AMINO ACID SEQUENCES.

Author

Wootton, John C. and Federhen, Scott

Subjects
AMINO acid sequence, TAXONOMY, PROTEIN genetics, MOLECULAR structure, COMPUTATIONAL biology
Published
1995

17. National Center for Biotechnology Information Viral Genomes Project.

Author

Yiming Bao, Federhen, Scott, Leipe, Detlef, Pham, Vyvy, Resechuk, Sergei, Rozanov, Mikhail, Tatusov, Roman, and Tatusova, Tatiana

Subjects
*VIRAL genetics, *BIOTECHNOLOGY, *GENOMES, *MOLECULAR genetics, *INFORMATION retrieval, *INFORMATION resources management
Abstract

Describes the National Center for Biotechnology Information Viral Genomes Project which aims to provide molecular standards for more than 1,200 different species. Information retrieval; Manual correction of Reference Sequence (RefSeq) records; Multicomponent viruses; Curatorial process for a virus RefSeq record.

Published
2004
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18. Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records.

Author

Federhen, Scott, Clark, Karen, Barrett, Tanya, Parkinson, Helen, Ostell, James, Kodama, Yuichi, Mashima, Jun, Nakamura, Yasukazu, Cochrane, Guy, and Karsch-Mizrachi, Ilene

Subjects
*METADATA, *TAXONOMY, *NUCLEOTIDE sequence, *DATABASES, *COMPUTER files
Abstract

Microbial genome sequence submissions to the International Nucleotide Sequence Database Collaboration (INSDC) have been annotated with organism names that include the strain identifier. Each of these strain-level names has been assigned a unique 'taxid' in the NCBI Taxonomy Database. With the significant growth in genome sequencing, it is not possible to continue with the curation of strain-level taxids. In January 2014, NCBI will cease assigning strain-level taxids. Instead, submitters are encouraged provide strain information and rich metadata with their submission to the sequence database, BioProject and BioSample. [ABSTRACT FROM AUTHOR]

Published
2014
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20. Comment on 'Birdstrikes and barcoding: can DNA methods help make the airways safer?'.

Author

FEDERHEN, SCOTT

Subjects
*AIRCRAFT bird collisions, *BIRD collisions, *DATABASES, *BAR codes, *DNA, *AIRWAYS (Aeronautics), *MOLECULAR ecology
Abstract

GenBank is the database of record for public sequence data. Results reported in the scientific literature that are based on sequence data cannot be evaluated if the underlying data is not in the public record. [ABSTRACT FROM AUTHOR]

Published
2011
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23. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

Author

Schoch CL, Robbertse B, Robert V, Vu D, Cardinali G, Irinyi L, Meyer W, Nilsson RH, Hughes K, Miller AN, Kirk PM, Abarenkov K, Aime MC, Ariyawansa HA, Bidartondo M, Boekhout T, Buyck B, Cai Q, Chen J, Crespo A, Crous PW, Damm U, De Beer ZW, Dentinger BT, Divakar PK, Dueñas M, Feau N, Fliegerova K, García MA, Ge ZW, Griffith GW, Groenewald JZ, Groenewald M, Grube M, Gryzenhout M, Gueidan C, Guo L, Hambleton S, Hamelin R, Hansen K, Hofstetter V, Hong SB, Houbraken J, Hyde KD, Inderbitzin P, Johnston PR, Karunarathna SC, Kõljalg U, Kovács GM, Kraichak E, Krizsan K, Kurtzman CP, Larsson KH, Leavitt S, Letcher PM, Liimatainen K, Liu JK, Lodge DJ, Luangsa-ard JJ, Lumbsch HT, Maharachchikumbura SS, Manamgoda D, Martín MP, Minnis AM, Moncalvo JM, Mulè G, Nakasone KK, Niskanen T, Olariaga I, Papp T, Petkovits T, Pino-Bodas R, Powell MJ, Raja HA, Redecker D, Sarmiento-Ramirez JM, Seifert KA, Shrestha B, Stenroos S, Stielow B, Suh SO, Tanaka K, Tedersoo L, Telleria MT, Udayanga D, Untereiner WA, Diéguez Uribeondo J, Subbarao KV, Vágvölgyi C, Visagie C, Voigt K, Walker DM, Weir BS, Weiß M, Wijayawardene NN, Wingfield MJ, Xu JP, Yang ZL, Zhang N, Zhuang WY, and Federhen S

Subjects
Cluster Analysis, DNA, Fungal, DNA, Intergenic, Genes, Fungal, Databases, Genetic, Fungi classification, Fungi genetics, Molecular Sequence Annotation methods, Sequence Analysis, DNA
Abstract

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated 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 during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353., (Published by Oxford University Press 2013. This work is written by US Government employees and is in the public domain in the US.)

Published
2014
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24. National center for biotechnology information viral genomes project.

Author

Bao Y, Federhen S, Leipe D, Pham V, Resenchuk S, Rozanov M, Tatusov R, and Tatusova T

Subjects
Animals, Base Sequence, Computational Biology, Humans, National Library of Medicine (U.S.), United States, Viral Proteins chemistry, Viral Proteins genetics, Viruses classification, Biotechnology, Databases, Genetic, Genome, Viral, Viruses genetics
Published
2004
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25. Discovering simple regions in biological sequences associated with scoring schemes.

Author

Wan H, Li L, Federhen S, and Wootton JC

Subjects
Aggrecans, Algorithms, Amino Acid Sequence, Collagen Type I chemistry, Collagen Type I genetics, Databases, Factual, Lectins, C-Type, Molecular Sequence Data, Molecular Structure, Myocardium metabolism, Myosin Heavy Chains chemistry, Myosin Heavy Chains genetics, Protein Conformation, Proteoglycans chemistry, Proteoglycans genetics, Sequence Alignment, Serine-tRNA Ligase genetics, Extracellular Matrix Proteins, Serine-tRNA Ligase chemistry, Thermus thermophilus enzymology
Abstract

Let A denote an alphabet consisting of n types of letters. Given a sequence S of length L with v(i) letters of type i on A, to describe the compositional properties and combinatorial structure of S, we propose a new complexity function of S, called the reciprocal complexity of S, as C(S) = (i=1) product operator (n) (L/nv(i))(vi) Based on this complexity measure, an efficient algorithm is developed for classifying and analyzing simple segments of protein and nucleotide sequence databases associated with scoring schemes. The running time of the algorithm is nearly proportional to the sequence length. The program DSR corresponding to the algorithm was written in C++, associated with two parameters (window length and cutoff value) and a scoring matrix. Some examples regarding protein sequences illustrate how the method can be used to find regions. The first application of DSR is the masking of simple sequences for searching databases. Queries masked by DSR returned a manageable set of hits below the E-value cutoff score, which contained all true positive homologues. The second application is to study simple regions detected by the DSR program corresponding to known structural features of proteins. An extensive computational analysis has been made of protein sequences with known, physicochemically defined nonglobular segments. For the SWISS-PROT amino acid sequence database (Release 40.2 of 02-Nov-2001), we determine that the best parameters and the best BLOSUM matrix are, respectively, for automatic segmentation of amino acid sequences into nonglobular and globular regions by the DSR program: Window length k = 35, cutoff value b = 0.46, and the BLOSUM 62.5 matrix. The average "agreement accuracy (sensitivity)" of DSR segmentation for the SWISS-PROT database is 97.3%.

Published
2003
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