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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

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

Author

Federhen, Scott, Federhen, Scott, Rossello-Mora, Ramon, Klenk, Hans-Peter, Tindall, Brian J., Konstantinidis, Konstantinos T., Whitman, William B., Brown, Daniel, Labeda, David, Ussery, David, Garrity, George M., Colwell, Rita R., Hasan, Nur, Graf, Joerg, Parte, Aidan, Yarza, Pablo, Goldberg, Brittany, Sichtig, Heike, Karsch-Mizrachi, Ilene, Clark, Karen, McVeigh, Richard, Pruitt, Kim D., Tatusova, Tatiana, Falk, Robert, Turner, Seán, Madden, Thomas, Kitts, Paul, Kimchi, Avi, Klimke, William, Agarwala, Richa, DiCuccio, Michael, Ostell, James, Federhen, Scott, Federhen, Scott, Rossello-Mora, Ramon, Klenk, Hans-Peter, Tindall, Brian J., Konstantinidis, Konstantinos T., Whitman, William B., Brown, Daniel, Labeda, David, Ussery, David, Garrity, George M., Colwell, Rita R., Hasan, Nur, Graf, Joerg, Parte, Aidan, Yarza, Pablo, Goldberg, Brittany, Sichtig, Heike, Karsch-Mizrachi, Ilene, Clark, Karen, McVeigh, Richard, Pruitt, Kim D., Tatusova, Tatiana, Falk, Robert, Turner, Seán, Madden, Thomas, Kitts, Paul, Kimchi, Avi, Klimke, William, Agarwala, Richa, DiCuccio, Michael, and Ostell, James

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.

Published
2016

17. Additional file 1: Figure S1. of Meeting report: GenBank microbial genomic taxonomy workshop (12â 13 May, 2015)

Author

Federhen, Scott, Rossello-Mora, Ramon, Hans-Peter Klenk, Tindall, Brian, Konstantinidis, Konstantinos, Whitman, William, Brown, Daniel, Labeda, David, Ussery, David, Garrity, George, Colwell, Rita, Hasan, Nur, Joerg Graf, Parte, Aidan, Yarza, Pablo, Goldberg, Brittany, Sichtig, Heike, Karsch-Mizrachi, Ilene, Clark, Karen, McVeigh, Richard, Pruitt, Kim, Tatusova, Tatiana, Falk, Robert, SeĂĄn Turner, Madden, Thomas, Kitts, Paul, Kimchi, Avi, Klimke, William, Agarwala, Richa, DiCuccio, Michael, and Ostell, James

Subjects
body regions, nervous system, fungi
Abstract

A Modest Proposal for making the Genomes of GenBank beneficial to the Publick, and preventing them from being a Burthen to the Curators and Taxonomists. (PDF 9956Â kb)

Published
2016
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18. Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015)

Author

Federhen, Scott, primary, Rossello-Mora, Ramon, additional, Klenk, Hans-Peter, additional, Tindall, Brian J., additional, Konstantinidis, Konstantinos T., additional, Whitman, William B., additional, Brown, Daniel, additional, Labeda, David, additional, Ussery, David, additional, Garrity, George M., additional, Colwell, Rita R., additional, Hasan, Nur, additional, Graf, Joerg, additional, Parte, Aidan, additional, Yarza, Pablo, additional, Goldberg, Brittany, additional, Sichtig, Heike, additional, Karsch-Mizrachi, Ilene, additional, Clark, Karen, additional, McVeigh, Richard, additional, Pruitt, Kim D., additional, Tatusova, Tatiana, additional, Falk, Robert, additional, Turner, Seán, additional, Madden, Thomas, additional, Kitts, Paul, additional, Kimchi, Avi, additional, Klimke, William, additional, Agarwala, Richa, additional, DiCuccio, Michael, additional, and Ostell, James, additional

Published
2016
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20. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

Author

Schoch, Conrad L., Robbertse, Barbara, Robert, Vincent, Duong Vu, [No Value], Cardinali, Gianluigi, Irinyi, Laszlo, Meyer, Wieland, Nilsson, R. Henrik, Hughes, Karen, Miller, Andrew N., Kirk, Paul M., Abarenkov, Kessy, Aime, M. Catherine, Ariyawansa, Hiran A., Bidartondo, Martin, Boekhout, Teun, Buyck, Bart, Cai, Qing, Chen, Jie, Crespo, Ana, Crous, Pedro W., Damm, Ulrike, De Beer, Z. Wilhelm, Dentinger, Bryn T. M., Divakar, Pradeep K., Duenas, Margarita, Feau, Nicolas, Fliegerova, Katerina, Garcia, Miguel A., Ge, Zai-Wei, Griffith, GarethW., Groenewald, Johannes Z., Groenewald, Marizeth, Grube, Martin, Gryzenhout, Marieka, Gueidan, Cecile, Guo, Liangdong, Hambleton, Sarah, Hamelin, Richard, Hansen, Karen, Hofstetter, Valerie, Hong, Seung-Beom, Houbraken, Jos, Hyde, Kevin D., Inderbitzin, Patrik, Johnston, Peter R., Karunarathna, Samantha C., Koljalg, Urmas, Kovacs, Gabor M., Kraichak, Ekaphan, Krizsan, Krisztina, Kurtzman, Cletus P., Larsson, Karl-Henrik, Leavitt, Steven, Letcher, Peter M., Liimatainen, Kare, Liu, Jian-Kui, Lodge, D. Jean, Luangsa-ard, Janet Jennifer, Lumbsch, H. Thorsten, Maharachchikumbura, Sajeewa S. N., Manamgoda, Dimuthu, Martin, Maria P., Minnis, Andrew M., Moncalvo, Jean-Marc, Mule, Giuseppina, Nakasone, Karen K., Niskanen, Tuula, Olariaga, Ibai, Papp, Tamas, Petkovits, Tamas, Pino-Bodas, Raquel, Powell, Martha J., Raja, Huzefa A., Redecker, Dirk, Sarmiento-Ramirez, J. M., Seifert, Keith A., Shrestha, Bhushan, Stenroos, Soili, Stielow, B., Suh, Sung-Oui, Tanaka, Kazuaki, Tedersoo, Leho, Teresa Telleria, M., Udayanga, Dhanushka, Untereiner, Wendy A., Dieguez Uribeondo, Javier, Subbarao, Krishna V., Vagvoelgyi, Csaba, Visagie, Cobus, Voigt, Kerstin, Walker, Donald M., Weir, Bevan S., Weiss, Michael, Wijayawardene, Nalin N., Wingfield, Michael J., Xu, J. P., Yang, Zhu L., Zhang, Ning, Zhuang, Wen-Ying, Federhen, Scott, Schoch, Conrad L., Robbertse, Barbara, Robert, Vincent, Duong Vu, [No Value], Cardinali, Gianluigi, Irinyi, Laszlo, Meyer, Wieland, Nilsson, R. Henrik, Hughes, Karen, Miller, Andrew N., Kirk, Paul M., Abarenkov, Kessy, Aime, M. Catherine, Ariyawansa, Hiran A., Bidartondo, Martin, Boekhout, Teun, Buyck, Bart, Cai, Qing, Chen, Jie, Crespo, Ana, Crous, Pedro W., Damm, Ulrike, De Beer, Z. Wilhelm, Dentinger, Bryn T. M., Divakar, Pradeep K., Duenas, Margarita, Feau, Nicolas, Fliegerova, Katerina, Garcia, Miguel A., Ge, Zai-Wei, Griffith, GarethW., Groenewald, Johannes Z., Groenewald, Marizeth, Grube, Martin, Gryzenhout, Marieka, Gueidan, Cecile, Guo, Liangdong, Hambleton, Sarah, Hamelin, Richard, Hansen, Karen, Hofstetter, Valerie, Hong, Seung-Beom, Houbraken, Jos, Hyde, Kevin D., Inderbitzin, Patrik, Johnston, Peter R., Karunarathna, Samantha C., Koljalg, Urmas, Kovacs, Gabor M., Kraichak, Ekaphan, Krizsan, Krisztina, Kurtzman, Cletus P., Larsson, Karl-Henrik, Leavitt, Steven, Letcher, Peter M., Liimatainen, Kare, Liu, Jian-Kui, Lodge, D. Jean, Luangsa-ard, Janet Jennifer, Lumbsch, H. Thorsten, Maharachchikumbura, Sajeewa S. N., Manamgoda, Dimuthu, Martin, Maria P., Minnis, Andrew M., Moncalvo, Jean-Marc, Mule, Giuseppina, Nakasone, Karen K., Niskanen, Tuula, Olariaga, Ibai, Papp, Tamas, Petkovits, Tamas, Pino-Bodas, Raquel, Powell, Martha J., Raja, Huzefa A., Redecker, Dirk, Sarmiento-Ramirez, J. M., Seifert, Keith A., Shrestha, Bhushan, Stenroos, Soili, Stielow, B., Suh, Sung-Oui, Tanaka, Kazuaki, Tedersoo, Leho, Teresa Telleria, M., Udayanga, Dhanushka, Untereiner, Wendy A., Dieguez Uribeondo, Javier, Subbarao, Krishna V., Vagvoelgyi, Csaba, Visagie, Cobus, Voigt, Kerstin, Walker, Donald M., Weir, Bevan S., Weiss, Michael, Wijayawardene, Nalin N., Wingfield, Michael J., Xu, J. P., Yang, Zhu L., Zhang, Ning, Zhuang, Wen-Ying, and Federhen, Scott

Published
2014

21. Finding needles in haystacks: Linking scientific names, reference specimens and molecular data for Fungi

Author

Schoch, C. L., Robbertse, B., Robert, V., Vu, D., Cardinali, G., Irinyi, L., Meyer, W., Nilsson, R. H., Hughes, K., Miller, A. N., Kirk, P.M., Tedersoo, Leho, Tellería, M. T., Udayanga, D., Untereiner, W. A., Uribeondo, J. D., Subbarao, K. V., Vágvölgyi, C., Visagie, C., Voigt, K., Walker, D. M., Weir, B. S., Weiß, M., Wijayawardene, Nalin N., Wingfield, M. J., Xu, J. P., Yang, Z. L., Zhang, N., Zhuang, W.-Y., Federhen, Scott, Abarenkov, K., Aime, M. C., Ariyawansa, H.A., Bidartondo, M., Boekhout, T., Buyck, B., Cai, Q., Chen, J., Crespo, A., Crous, P. W., Damm, U., de Beer, Z.W., Dentinger, B. T. M., Divakar, Pradeep K., Dueñas, Margarita, Feau, N., Fliegerova, K., García, M. A., Ge, Z.-W., Griffith, G.W., Groenewald, J. Z., Groenewald, M., Grube, M., Gryzenhout, M., Gueidan, C., Guo, L., Hambleton, S., Hamelin, R., Hansen, K., Hofstetter, V., Hong, S.-B., Houbraken, J., Hyde, K.D., Inderbitzin, P., Johnston, P. R., Karunarathna, S. C., Kõljalg, Urmas, Kovacs, G., Kraichak, E., Krizsan, K., Kurtzman, Cletus P., Larsson, Karl-Henrik, Leavitt, S., Letcher, P. M., Liimatainen, K., Liu, J.-K., Lodge, D. J., Luangsa-Ard, J. J., Lumbsch, H.T., Maharachchikumbura, Sajeewa S. N., Manamgoda, D. S., Martín, María P., Minnis, A. M., Moncalvo, J.-M., Mulè, G., Nakasone, K. K., Niskanen, T., Olariaga, I., Papp, T., Petkovits, T., Pino Bodas, Raquel, Powell, M. J., Raja, H.A., Redecker, D., Sarmiento Ramírez, Jullie Melissa, Seifert, K. A., Shrestha, B., Stenroos, S., Stielow, B., Suh, S.-O., Tanaka, K., Schoch, C. L., Robbertse, B., Robert, V., Vu, D., Cardinali, G., Irinyi, L., Meyer, W., Nilsson, R. H., Hughes, K., Miller, A. N., Kirk, P.M., Tedersoo, Leho, Tellería, M. T., Udayanga, D., Untereiner, W. A., Uribeondo, J. D., Subbarao, K. V., Vágvölgyi, C., Visagie, C., Voigt, K., Walker, D. M., Weir, B. S., Weiß, M., Wijayawardene, Nalin N., Wingfield, M. J., Xu, J. P., Yang, Z. L., Zhang, N., Zhuang, W.-Y., Federhen, Scott, Abarenkov, K., Aime, M. C., Ariyawansa, H.A., Bidartondo, M., Boekhout, T., Buyck, B., Cai, Q., Chen, J., Crespo, A., Crous, P. W., Damm, U., de Beer, Z.W., Dentinger, B. T. M., Divakar, Pradeep K., Dueñas, Margarita, Feau, N., Fliegerova, K., García, M. A., Ge, Z.-W., Griffith, G.W., Groenewald, J. Z., Groenewald, M., Grube, M., Gryzenhout, M., Gueidan, C., Guo, L., Hambleton, S., Hamelin, R., Hansen, K., Hofstetter, V., Hong, S.-B., Houbraken, J., Hyde, K.D., Inderbitzin, P., Johnston, P. R., Karunarathna, S. C., Kõljalg, Urmas, Kovacs, G., Kraichak, E., Krizsan, K., Kurtzman, Cletus P., Larsson, Karl-Henrik, Leavitt, S., Letcher, P. M., Liimatainen, K., Liu, J.-K., Lodge, D. J., Luangsa-Ard, J. J., Lumbsch, H.T., Maharachchikumbura, Sajeewa S. N., Manamgoda, D. S., Martín, María P., Minnis, A. M., Moncalvo, J.-M., Mulè, G., Nakasone, K. K., Niskanen, T., Olariaga, I., Papp, T., Petkovits, T., Pino Bodas, Raquel, Powell, M. J., Raja, H.A., Redecker, D., Sarmiento Ramírez, Jullie Melissa, Seifert, K. A., Shrestha, B., Stenroos, S., Stielow, B., Suh, S.-O., and Tanaka, K.

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. Reannotated 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.

Published
2014

22. Update on RefSeq microbial genomes resources

Author

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

Published
2014
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30. 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

31. 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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32. 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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