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1. Database resources of the National Center for Biotechnology Information

Author

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

Subjects
Internet, 0303 health sciences, National Library of Medicine (U.S.), Computational Biology, Information Storage and Retrieval, Genome, Viral, Articles, United States, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, National Institutes of Health (U.S.), 030220 oncology & carcinogenesis, Databases, Genetic, Genetics, Animals, Humans, natural sciences, Databases, Nucleic Acid, Databases, Protein, Algorithms, Genome, Bacterial, Software, 030304 developmental biology
Abstract

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, Reference Sequence, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Peptidome, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Published
2009
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2. The ORFeome Collaboration: a genome-scale human ORF-clone resource

Author

Anja van Brabant Smith, Ruth Wellenreuther, Shuwei Yang, Sun Lu, Gary F. Temple, Yoshihide Hayashizaki, Jin Park, J. Wade Harper, Yanhui Hu, Oliver Heil, Tong Hao, Jun Kawai, Blake A. Simmons, Kourosh Salehi-Ashtiani, Christoph Koenig, Ian Dunham, Catherine Seiler, Steffen Hennig, Anika Jöcker, Piero Carninci, Cristen Lambert, Troy Moore, Anita Lebeau, David E. Hill, Melanie Busse, Tom Weaver, Preston Hunter, Wonhee Jang, Matthias Harbers, Marc Vidal, Graeme Bethel, Mark Diekhans, Osamu Ohara, Bernhard Korn, Joshua La Baer, Lukas Wagner, Alexandra Amiet, Daniela S. Gerhard, Andreas Rolfs, Johannes Maurer, Christa Pennacchio, Jason Steel, Stefan Wiemann, and Agnes Hotz-Wagenblatt

Subjects
0301 basic medicine, Internet, Resource (biology), Proteome, Genome, Human, Clone (cell biology), Genome scale, Cell Biology, Computational biology, Biology, Biochemistry, Clone Cells, Open Reading Frames, User-Computer Interface, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, 030220 oncology & carcinogenesis, Databases, Genetic, Database Management Systems, Humans, Cloning, Molecular, ORFeome, Molecular Biology, Biotechnology
Published
2016
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3. The completion of the Mammalian Gene Collection (MGC)

Author

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

Subjects
Resource, DNA, Complementary, Biology, chemistry.chemical_compound, Mice, Genetics, RefSeq, Animals, Humans, Genomic library, Cloning, Molecular, Gene, Genetics (clinical), Gene Library, Cloning, Mammals, Expressed sequence tag, DNA synthesis, cDNA library, Reverse Transcriptase Polymerase Chain Reaction, Computational Biology, DNA, United States, Rats, chemistry, Genes, National Institutes of Health (U.S.)
Abstract

Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97% of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible without restriction to researchers worldwide.

Published
2009

4. Resources for genetic and genomic studies of Xenopus

Author

Steven L, Klein, Daniela S, Gerhard, Lukas, Wagner, Paul, Richardson, Lynn M, Schriml, Amy K, Sater, Wesley C, Warren, and John D, McPherson

Subjects
Internet, National Institutes of Health (U.S.), National Library of Medicine (U.S.), Xenopus, Animals, Computational Biology, Humans, Genomics, United States, Developmental Biology, Gene Library
Abstract

The National Institutes of Health Xenopus Initiative is a concerted effort to interact with the Xenopus research community to identify the community's needs; to devise strategies to meet those needs; and to support, oversee, and coordinate the resulting projects. This chapter provides a brief description of several genetic and genomic resources generated by this initiative and explains how to access them. The resources described in this chapter are (1) complementary deoxyribonucleic acid (cDNA) libraries and expressed sequence tag (EST) sequences; (2) UniGene clusters; (3) full-insert cDNA sequences; (4) a genetic map; (5) genomic libraries; (6) a physical map; (7) genome sequence; (8) microarrays; (9) mutagenesis and phenotyping; and (10) bioinformatics. The descriptions presented here were based on data that were available at the time of manuscript submission. Because these are ongoing projects, they are constantly generating new data and analyses. The Web sites cited in each subheading present current data and analyses.

Published
2006

5. Resources for Genetic and Genomic Studies of Xenopus

Author

John Douglas Mcpherson, Steven L. Klein, Lukas Wagner, Paul G. Richardson, Daniela S. Gerhard, Lynn M. Schriml, Amy K. Sater, and Wesley C. Warren

Subjects
Whole genome sequencing, Expressed sequence tag, biology, Computer science, Complementary DNA, Mutagenesis, Xenopus, UniGene, Genomics, Genomic library, Computational biology, DNA microarray, biology.organism_classification
Abstract

The National Institutes of Health Xenopus Initiative is a concerted effort to interact with the Xenopus research community to identify the community's needs; to devise strategies to meet those needs; and to support, oversee, and coordinate the resulting projects. This chapter provides a brief description of several genetic and genomic resources generated by this initiative and explains how to access them. The resources described in this chapter are (1) complementary deoxyribonucleic acid (cDNA) libraries and expressed sequence tag (EST) sequences; (2) UniGene clusters; (3) full-insert cDNA sequences; (4) a genetic map; (5) genomic libraries; (6) a physical map; (7) genome sequence; (8) microarrays; (9) mutagenesis and phenotyping; and (10) bioinformatics. The descriptions presented here were based on data that were available at the time of manuscript submission. Because these are ongoing projects, they are constantly generating new data and analyses. The Web sites cited in each subheading present current data and analyses.

Published
2006
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6. The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)

Author

Yutaka Suzuki, Stephanie Rodrigues, Francis S. Collins, Agnes Baross, Jane Grimwood, Anna Sneed, Anuradha Madan, Sinnakaruppan Mathavan, Nicole Shapiro, Peggy N. Kwong, Martin Krzywinski, Chia-Lin Wei, Susan Old, Michael R. Brent, Jeff M. Stott, Jim Kent, Robert W. Blakesly, Steven J. Granite, Yaron S.N. Butterfield, Shiraki Toshiyuki, Jessica Fahey, Steven J.M. Jones, Eric D. Green, Jeffery G. Derge, Kirsten Schreiber, Todd E. Scheetz, Anup Madan, C. E. Gruber, Mark Ketteman, Sumio Sugano, Blake A. Simmons, Kathryn A. Makowski, Richard M. Myers, Michael J. Brownstein, David Haussler, Narayan K. Bhat, Minoru S.H. Ko, Thomas L. Casavant, Anca Petrescu, Eduardo Lee, Angela M. Garcia, Obi L. Griffith, David J. Lipman, Terry Furey, Peter J. Good, Koichi Kawakami, Ye Yuan, Jia Qian Wu, Keith Wetherby, Allison M. Peck, Angelique Schnerch, Piero Carninci, Robert A. Holt, Diana L. Palmquist, Amy Sanchez, Stephen L. Johnson, Maria de Fatima Bonaldo, Ursula Skalska, John Douglas Mcpherson, Michelle Whiting, Charles P. Brinkley, Alice C. Young, Elise A. Feingold, Dawood B. Dudekula, M. R. Smith, Joel A. Malek, Christa Prange, Jeremy Schmutz, Wonhee Jang, Richard A. Gibbs, Stephanie Bosak, Alex Rodriguez, Lukas Wagner, Yulan Piao, Mike Feolo, Leonie Misquitta, Donna M. Muzny, Mark S. Guyer, Tom I. Bonner, Florence Hsie, Rebekah S. Rasooly, Nancy Y. Liao, Preethi H. Gunaratne, Malachi Griffith, Troy Moore, Erin Helton, Daniela S. Gerhard, Richard C. Waterman, Ralph F. Hopkins, Kirill Rotmistrovsky, Mark Diekhans, Edwin Fuh, Greg Schuler, Carl F. Schaefer, Anne Hodgson, Gerard G. Bouffard, Sandra W. Clifton, Mark Dickson, Lynette H. Grouse, Tom Driscoll, Stephen W. Hulyk, Susan F. Greenhut, Carolyn M. Shenmen, Steven L. Klein, Duane E. Smailus, Yijun Ruan, Ted B. Usdin, Jacqueline E. Schein, Marco A. Marra, Ryan Morrin, M. Bento Soares, Steven Sherry, Russell L. Pearson, Carla Kowis, and Kenneth H. Buetow

Subjects
clone (Java method), DNA, Complementary, Biology, Mice, Open Reading Frames, Xenopus laevis, Complementary DNA, Genetics, Animals, Humans, Genomic library, Cloning, Molecular, Gene, Genetics (clinical), Zebrafish, DNA Primers, Gene Library, Cloning, cDNA library, Computational Biology, Resources, United States, Rats, Open reading frame, National Institutes of Health (U.S.), Reference genome
Abstract

The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5′-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline.

Published
2004

7. Open Mass Spectrometry Search Algorithm

Author

Lewis Y. Geer, Ming Xu, Stephen H. Bryant, Sanford P. Markey, Lukas Wagner, Dawn M. Maynard, Wenyao Shi, Jeffrey A. Kowalak, and Xiaoyu Yang

Subjects
Proteomics, Matching (graph theory), PeptideProphet, Analytical chemistry, Mass spectrometry, Biochemistry, Quantitative Biology - Quantitative Methods, Mass Spectrometry, Peptide spectral library, Search algorithm, Significance testing, False Positive Reactions, Poisson Distribution, Databases, Protein, Quantitative Methods (q-bio.QM), business.industry, Chemistry, Computational Biology, Proteins, Reproducibility of Results, Pattern recognition, General Chemistry, Peptide Fragments, ROC Curve, FOS: Biological sciences, Artificial intelligence, Mass spectrometry data format, business, Algorithms
Abstract

Large numbers of MS/MS peptide spectra generated in proteomics experiments require efficient, sensitive and specific algorithms for peptide identification. In the Open Mass Spectrometry Search Algorithm (OMSSA), specificity is calculated by a classic probability score using an explicit model for matching experimental spectra to sequences. At default thresholds, OMSSA matches more spectra from a standard protein cocktail than a comparable algorithm. OMSSA is designed to be faster than published algorithms in searching large MS/MS datasets. Keywords: protein identification • algorithm • bioinformatics • mass spectrometry • proteomics • significance testing

Published
2004

8. Annotation Marathon Validates 21,037 Human Genes

Author

Satoshi Oota, Marie-Dominique Devignes, Arek Kasprzyk, Inna Dubchak, Wojciech Makalowski, Anthony J. Brookes, Per Unneberg, Susan Bromberg, Naoki Nagata, Matthew I. Bellgard, Yasuyuki Fujii, Vladimir Kuryshev, Tetsuji Otsuki, Yoonsoo Hahn, Andrew J. G. Simpson, Ryuichi Sakate, Hyang-Sook Yoo, Minoru Kanehisa, Yoshiyuki Sakaki, Toshio Ota, Kaoru Fukami-Kobayashi, Tomohiro Yasuda, Janet Kelso, Ze-Guang Han, Paul J. Kersey, Lukas Wagner, Norikazu Yasuda, Ursula Hinz, Rolf Apweiler, Tadashi Imanishi, Yoshio Tateno, Hideo Matsuda, Ranajit Chakraborty, Danielle Thierry-Mieg, Nobuo Nomura, Toshihisa Okido, Elspeth A. Bruford, Sandrine Imbeaud, Hans-Werner Mewes, Toshinori Endo, Motohiko Tanino, Ingo Schupp, Hideki Hanaoka, Alexander Kanapin, Dominique Piatier-Tonneau, Craig A. Gough, Sangsoo Kim, Zhu Chen, Michael Han, Anne Estreicher, Sandro J. de Souza, Ken Nishikawa, Hideki Nagasaki, Masafumi Ohtsubo, Osamu Ohara, Reiko Kikuno, Roberto A. Barrero, Claude Chelala, Aiko Takahashi, Stefan Wiemann, Hiroaki Sakai, Satoshi Fukuchi, Takao Isogai, Eric Eveno, Nobuyoshi Shimizu, Mitiko Go, Charles A. Steward, Laurens G. Wilming, Hideaki Sugawara, Jennifer L. Ashurst, Maria de Fatima Bonaldo, Peter J. Tonellato, Gen Tamiya, Takuro Tamura, Michio Oishi, Shuang-Xi Ren, Toshihisa Takagi, Régine Mariage-Samson, Makiko Suwa, Phillip Hilton, Youla Karavidopoulou, Shuhei Mano, Rajni Nigam, Kei Yura, Todd D. Taylor, Norihiro Okada, John Quackenbush, Mitsuteru Nakao, Osamu Ogasawara, Kouichi Kimura, Yoshihide Hayashizaki, Marvin Stodolsky, Keiichi Nagai, Sumio Sugano, Joseph D. Terwilliger, Jun Mashima, Florence Servant, Yasushi Okazaki, Yoshiyuki Suzuki, Motonori Ota, Shinsei Minoshima, Momoki Hirai, Nicola Mulder, Esther Graudens, Stephen T. Sherry, Eduardo Eyras, Susumu Tanaka, Kanako O. Koyanagi, Katsunaga Sakai, Piero Carninci, Charles Auffray, Kazuho Ikeo, Hiroshi Tanaka, Hidemasa Bono, Vamsi Veeramachaneni, Mika Hirakawa, Shigetaka Sakamoto, Tetsuo Nishikawa, Takashi Gojobori, Yumi Yamaguchi-Kabata, Claire O'Donovan, Shinya Watanabe, Clara Amid, Mary Shimoyama, Mami Suzuki, Erimi Harada, Rie Shiba, Takeshi Itoh, Kousaku Okubo, Hidetoshi Inoko, Lihua Jin, Ian Hopkinson, Chisato Yamasaki, Teruyoshi Hishiki, Libin Jia, Winston Hide, Yutaka Suzuki, Keiichi Homma, Izabela Makalowska, Michael A. Thomas, Marie-Anne Debily, Annemarie Poustka, Satoru Miyazaki, Katsuyuki Hashimoto, Bento Soares, Robert L. Strausberg, Gopal R. Gopinath, Takeya Kasukawa, Boris Lenhard, Bernhard Korn, Christine Couillault, Jun-ichi Takeda, Jean Thierry-Mieg, Yayoi Kaneko, Takashi Makino, Kousuke Hanada, Kenta Nakai, and Naruya Saitou

Subjects
DNA, Complementary, Sequence analysis, QH301-705.5, Gene prediction, ADN, Biology, Genetics/Genomics/Gene Therapy, Polymorphism, Single Nucleotide, Genome, General Biochemistry, Genetics and Molecular Biology, Open Reading Frames, 03 medical and health sciences, 0302 clinical medicine, Gene mapping, Homo (Human), Databases, Genetic, Gene cluster, Humans, Bioinformatics/Computational Biology, Biology (General), Gene, 030304 developmental biology, Genetics, Internet, 0303 health sciences, Polymorphism, Genetic, General Immunology and Microbiology, Genome, Human, General Neuroscience, Alternative splicing, Computational Biology, Protein Structure, Tertiary, Alternative Splicing, Genes, 030220 oncology & carcinogenesis, Human genome, General Agricultural and Biological Sciences, Microsatellite Repeats, Research Article, Gens
Abstract

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology., An international team has systematically validated and annotated just over 21,000 human genes using full-length cDNA, thereby providing a valuable new resource for the human genetics community

Published
2004

9. Database resources of the National Center for Biotechnology Information: update

Author

Deanna M. Church, Lukas Wagner, Ron Edgar, Tatiana Tatusova, Wolfgang Helmberg, David L. Wheeler, Joan Pontius, Lynn M. Schriml, Tugba O. Suzek, Thomas L. Madden, Scott Federhen, Edwin Sequeira, and Gregory D. Schuler

Subjects
PubMed, Databases, Factual, Conserved Domain Database, UniGene, Information Storage and Retrieval, Biology, computer.software_genre, Open Reading Frames, Genetics, RefSeq, Animals, Humans, natural sciences, Molecular Modeling Database, Sequence profiling tool, Genome, Polymorphism, Genetic, Database, business.industry, Entrez Gene, Gene Expression Profiling, Computational Biology, Genomics, Articles, Classification, United States, Biotechnology, Entrez, body regions, Genes, National Institutes of Health (U.S.), GenBank, business, computer, Software
Abstract

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's website. NCBI resources include Entrez, PubMed, PubMed Central, LocusLink, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SARS Coronavirus Resource, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD) and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.

Published
2003

10. Functional annotation of a full-length mouse cDNA collection

Author

S. Fukuda, F. Staubli, Yasushi Okazaki, Harukazu Suzuki, W. Fleischmann, Lynn M. Schriml, Yoshifumi Fukunishi, Charles A. Whittaker, Hideaki Konno, Koji Kadota, Christian Schönbach, Yoshihide Hayashizaki, J. Mazzarelli, S. Kondo, Carmela Gissi, Judith A. Blake, K. Sato, Manuela Gariboldi, Y. Ishii, R. Suzuki, David A. Hume, Y. Matsuo, Peter Mombaerts, N. Bojunga, Michael J. Brownstein, P. Kuehl, Akira Shinagawa, Masaru Tomita, Carol J. Bult, Masaki Fujita, Masayasu Yoshino, P. Nordone, H. Aono, Terry Gaasterland, Benjamin L. King, Masaki Izawa, Luigi Marchionni, Paul A. Lyons, Takanori Washio, Simon L. Lewis, David E. Hill, Itoshi Nikaido, Kuan Hong Wang, Kazuhito Toyo-oka, Thomas L. Casavant, Y. Hasegawa, Piero Carninci, Richard M. Baldarelli, Hidemasa Bono, Jun Kawai, Brian Z. Ring, Toshihisa Okido, H. Sasaki, Hideo Matsuda, Hideya Kawaji, John Quackenbush, L. Wilming, Marion A. Hofmann, M. F. De Bonaldo, Graziano Pesole, Takashi Saito, Lukas Wagner, Dario Boffelli, Takahiro Arakawa, Jun Adachi, K. Yoshida, Charles J. Weitz, Norman H. Lee, Naoaki Sakamoto, Michael Ashburner, A. Hara, Hiromi Kochiwa, Masaaki Furuno, Katsunori Aizawa, Ivan Rodriguez, Itaru Yamanaka, H. Kiyosawa, Anthony Wynshaw-Boris, Kenichiro Nishi, Gregory S. Barsh, Takashi Gojobori, Kai-Florian Storch, Jun Mashima, Takeya Kasukawa, Mamoru Kamiya, Tsukasa Seya, Stefano Gustincich, K. Sakai, Y. Shibata, M. Ringwald, Christopher D.M. Fletcher, Rintaro Saito, Serge Batalov, S. Kohtsuki, Masayoshi Itoh, and K. Shibata

Subjects
DNA, Complementary, Sequence analysis, Biology, Genome, Mice, Complementary DNA, Animals, Humans, Gene family, Genomic library, RNA, Messenger, Gene, Gene Library, computer.programming_language, Genetics, Cloning, Multidisciplinary, Chromosome Mapping, Computational Biology, Fantom, Sequence Analysis, DNA, Enzymes, Protein Structure, Tertiary, Mice, Inbred C57BL, Protein Biosynthesis, computer
Abstract

The RIKEN Mouse Gene Encyclopaedia Project, a systematic approach to determining the full coding potential of the mouse genome, involves collection and sequencing of full-length complementary DNAs and physical mapping of the corresponding genes to the mouse genome. We organized an international functional annotation meeting (FANTOM) to annotate the first 21,076 cDNAs to be analysed in this project. Here we describe the first RIKEN clone collection, which is one of the largest described for any organism. Analysis of these cDNAs extends known gene families and identifies new ones.

Published
2001

11. SAGEmap: A Public Gene Expression Resource

Author

Alex E. Lash, Gregory D. Schuler, Robert L. Strausberg, Gregory J. Riggins, Lukas Wagner, Carolyn M. Tolstoshev, and Stephen F. Altschul

Subjects
Resource, Male, File Transfer Protocol, Databases, Factual, Gene Expression, Computational biology, Biology, Bioinformatics, Sequence-tagged site, Gene expression, Genetics, Humans, Serial analysis of gene expression, Genetics (clinical), Cancer Genome Anatomy Project, Gene Library, Sequence Tagged Sites, Internet, business.industry, SAGE, fungi, Signal Processing, Computer-Assisted, Sequence Analysis, DNA, The Internet, Female, DNA microarray, business
Abstract

Gene expression quantifying techniques promise to shape our understanding of the distribution and regulation of the products of transcription in normal and abnormal cell types. cDNA microarray (DeRisi 1997), high-density oligo DNA array (Wodicka 1997) and serial analysis of gene expression (Velculescu 1995) techniques have all been developed to quickly and efficiently survey genome-wide transcript expression. However, each of these techniques has the potential to produce, in a single experiment, vast amounts of data which must be sifted and ordered for useful information to become apparent. Additional challenges are met when attempts are made to compare, merge and contrast data from experiments conducted under differing conditions and locales. As a prototype for the handling, analysis and exchange of gene expression data in the public forum, we have undertaken the production of a public repository and resource for a particular set of gene expression data, i.e., serial analysis of gene expression (SAGE) data. This repository was designed initially to archive SAGE data produced through the Cancer Genome Anatomy Project (CGAP) (Strausberg 1997; http://www.ncbi.nlm.nih.gov/cgap) but is now capable of accepting submissions of SAGE sequence data from any source, without fee or restriction on dissemination or use. It is our goal to provide free and open access to raw SAGE sequence data, precomputed tag extractions, and several modest analysis tools. This resource currently contains over two million tags from 47 SAGE libraries. We call this resource SAGEmap. Its two online components are available via the World Wide Web (http://www.ncbi.nlm.nih.gov/sage) and anonymous FTP (ftp://ncbi.nlm.nih.gov/pub/sage).

Published
2000

12. Correction: Initial sequencing and analysis of the human genome

Author

Paul Predki, John Sulston, William Morris, Sarah Wenning, Jun Gu, Danielle Thierry-Mieg, Roger A. Schultz, Michael J. Morgan, Michael Doyle, Joseph Szustakowki, Lorenzo Cerutti, A. Coulson, Alex Bateman, Patrick Wincker, Michael C. Zody, Mark T. Ross, Paul G. Richardson, Keri Devon, Yasushi Totoki, Karsten Hokamp, George M. Weinstock, John Howland, Arek Kaspryzk, James G. R. Gilbert, Cher Miranda, Aristides Patrinos, William Saurin, A. Pia Abola, Kazuhiko Kawasaki, John Bouck, Marvin Frazier, Wonhee Jang, Jan Fang Cheng, Stephanie L. Chissoe, Matthew C. Jones, Glen A. Evans, Huanming Yang, Daniel G. Brown, Richard Durbin, Jennifer Baldwin, Tracie L. Miner, Asif T. Chinwalla, Arian F.A. Smit, C M Clee, Elaine R. Mardis, Henning Hermjakob, Nicole Stange-Thomann, Maynard V. Olson, Jian Wang, Cyrus L. Harmon, Shiaw Pyng Yang, André Rosenthal, Catherine Robert, Masahira Hattori, Jane Peterson, Ratna Shownkeen, Maria Athanasiou, Christopher B. Burge, Erica Sodergren, Carrie Sougnez, Lynn Doucette-Stamm, Hidemi Watanabe, Ronald W. Davis, Tarjei S. Mikkelsen, Mark Rosetti, Christopher J. Elkin, Todd M. Lowe, LaDeana W. Hillier, Jane Grimwood, Kazutoyo Osoegawa, Richard R. Copley, Simon Kasif, Joseph J. Catanese, Keith Weinstock, Lee Rowen, Roel Funke, Paul Kitts, Lukas Wagner, Guy Slater, Anne S. Olsen, Edward Uberbacher, Lucinda Fulton, Andrew Dunham, Andrew Heaford, David Kulp, Elbert Branscomb, William Fitzhugh, Eugene V. Koonin, Leroy Hood, Anup Madan, Jean Thierry-Mieg, Richard Reinhardt, Kim C. Worley, Richard M. Myers, Dudley Wyman, Jean Weissenbach, David R. Bentley, Panos Deloukas, Philippe Brottier, H. Blöcker, Stephan Beck, Marc Rubenfield, Terrence S. Furey, Ken Dewar, Michael L. Metzker, Rajinder Kaul, Guyang Huang, Hsiu Chuan Chen, Ewan Birney, Warren Gish, John Douglas Mcpherson, Asao Fujiyama, Aoife McLysaght, Shinsei Minoshima, Sandra W. Clifton, Lisa Kann, R Ainscough, K. Hornischer, Simon G. Gregory, Lauren Linton, Kim D. Delehaunty, James C. Mullikin, Neilay Dedhia, Matthias Platzer, Gerald Nyakatura, John V. Moran, Andrew J. Mungall, Chiharu Kawagoe, François Artiguenave, Deanna M. Church, Elia Stupka, Jun Yu, Peer Bork, Evan E. Eichler, L. Aravind, James H. Gorrell, Bruce A. Roe, Raymond Wheeler, Norman A. Doggett, Douglas R. Smith, Yu Juin Chen, David Haussler, Todd D. Taylor, Stefan Taudien, Susan Lucas, Rebecca Deadman, Hans Lehrach, Hiroaki Shizuya, Doron Lancet, Greg Schuler, Nigel P. Carter, John Burton, Huaqin Pan, Eric S. Lander, Andreas Rump, Nikola Stojanovic, Victor J. Pollara, Alan Williams, Melissa De La Bastide, W. James Kent, Mark S. Guyer, Nicola Mulder, Sarah Milne, Bruce W. Birren, John W. Wallis, Joann Dubois, Tom Slezak, Lisa Cook, Raju Kucherlapati, Andrew Delehaunty, Lucy Matthews, Ian Dunham, L. Steven Johnson, Robert H. Waterston, Andrew Sheridan, Jörg Schultz, Nancy A. Federspiel, Jason B. Kramer, Tim Hubbard, Ru Fang Yeh, Steven E. Scherer, Francis S. Collins, David L. Nelson, Sean Humphray, Tobias Doerks, Chad Nusbaum, Darren Grafham, Mei Lee Hong, Michael Proctor, Christopher K. Raymond, Diane Gage, Kris A. Wetterstrand, Feng Chen, Simon Mercer, Thomas A. Jones, Trevor Hawkins, Aravind Subramanian, Jeffrey A. Bailey, Amanda McMurray, Serafim Batzoglou, Jeremy Schmutz, Jill P. Mesirov, Shizen Qin, Rosie Levine, Adam Felsenfeld, Thomas Brüls, Kevin McKernan, Michele E. Clamp, Christine Lloyd, Susan L. Naylor, Gabriele Nordsiek, Jessica A. Lehoczky, Adrienne Hunt, Marco A. Marra, David R. Cox, Mark Dickson, Michael C. Wendl, Yuri I. Wolf, Jane Rogers, Ian F Korf, Eric Pelletier, Takehiko Itoh, Juliane Ramser, Robert S. Fulton, Sarah Sims, Richard A. Gibbs, Lisa French, Katrina Harris, Richa Agarwala, Christina Raymond, James Meldrim, Sangdun Choi, Richard K. Wilson, Patrick Minx, Douglas L. Johnson, Yoshiyuki Sakaki, Scot Kennedy, Pieter J. de Jong, Yoshihide Hayashizaki, W. Richard McCombie, Sean R. Eddy, Donna M. Muzny, Jerome Naylor, Paul A. McEwan, Atsushi Toyoda, Tetsushi Yada, Nobuyoshi Shimizu, Robert W. Plumb, Catherine M. Rives, Chris P. Ponting, Ralph Santos, Kenneth H. Wolfe, Kymberlie H. Pepin, Roland Heilig, and James E. Galagan

Subjects
Multidisciplinary, Correction, Human genome, Computational biology, Biology
Published
2001
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