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GenBank

Karen Clark, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers
2015 Nucleic Acids Research  
GenBank R (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 340 000 formally described species. Recent developments include a new starting page for submitters, a shift toward using accession.version identifiers rather than GI numbers, a wizard for submitting 16S rRNA sequences, and an Identical Protein Report to address growing issues of data redundancy. GenBank organizes the sequence data received from individual
more » ... ies and largescale sequencing projects into 18 divisions, and Gen-Bank staff assign unique accession.version identifiers upon data receipt. Most submitters use the web-based BankIt or standalone Sequin programs. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the nuccore, nucest, and nucgss databases of the Entrez retrieval system, which integrates these records with a variety of other data including taxonomy nodes, genomes, protein structures, and biomedical journal literature in PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP.
doi:10.1093/nar/gkv1276 pmid:26590407 pmcid:PMC4702903 fatcat:czyvsrb4gffjfop3wlvryqj7km

GenBank

Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers
2009 Nucleic Acids Research  
GenBank Õ is a comprehensive database that contains publicly available nucleotide sequences for more than 300 000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff
more » ... n receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bi-monthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI homepage: www.ncbi.nlm.nih.gov.
doi:10.1093/nar/gkp1024 pmid:19910366 pmcid:PMC2808980 fatcat:5hx2nirjdjbrfj3khqjbfp5avq

GenBank

Dennis A. Benson, Karen Clark, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers
2013 Nucleic Acids Research  
Tel: +1 301 496 2475; Fax: +1 301 480 9241; Email: sayers@ncbi.nlm.nih.gov Table 1 . 1 Growth of GenBank divisions (nucleotide base pairs) Division Description Release 197 (8/2013) Annual increase  ... 
doi:10.1093/nar/gkt1030 pmid:24217914 pmcid:PMC3965104 fatcat:wjdyeblmtbh2nchbemgybvfsle

GenBank

Dennis A. Benson, Karen Clark, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers
2014 Nucleic Acids Research  
GenBank R (http://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 300 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from largescale sequencing projects, including whole-genome shotgun and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assign
more » ... accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP.
doi:10.1093/nar/gku1216 pmid:25414350 pmcid:PMC4383990 fatcat:rrzuod6pgrah3hq4nyuy6bzpyy

GenBank

Eric W Sayers, Mark Cavanaugh, Karen Clark, Kim D Pruitt, Conrad L Schoch, Stephen T Sherry, Ilene Karsch-Mizrachi
2020 Nucleic Acids Research  
GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 9.9 trillion base pairs from over 2.1 billion nucleotide sequences for 478 000 formally described species. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. Recent updates include new resources for data from the SARS-CoV-2 virus, updates to the NCBI Submission Portal and associated submission wizards for dengue and SARS-CoV-2
more » ... , new taxonomy queries for viruses and prokaryotes, and simplified submission processes for EST and GSS sequences.
doi:10.1093/nar/gkaa1023 pmid:33196830 fatcat:og3arru36vax7kckaozbjokxtq

GenBank

Dennis A. Benson, Mark Cavanaugh, Karen Clark, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers
2016 Nucleic Acids Research  
GenBank ® (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for 370 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or the NCBI Submission Portal. GenBank staff assign
more » ... numbers upon data receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Nucleotide database, which links to related information such as taxonomy, genomes, protein sequences and structures, and biomedical journal literature in PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. Recent updates include changes to policies regarding sequence identifiers, an improved 16S submission wizard, targeted loci studies, the ability to submit methylation and BioNano mapping files, and a database of anti-microbial resistance genes.
doi:10.1093/nar/gkw1070 pmid:27899564 pmcid:PMC5210553 fatcat:u2pjbbcpwvgifdolo6wmqt5vvi

GenBank

Dennis A Benson, Mark Cavanaugh, Karen Clark, Ilene Karsch-Mizrachi, James Ostell, Kim D Pruitt, Eric W Sayers
2017 Nucleic Acids Research  
GenBank ® (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for 400 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun and environmental sampling projects. Most submissions are made using BankIt, the National Center for Biotechnology Information (NCBI) Submission Portal, or
more » ... he tool tbl2asn. GenBank staff assign accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Nucleotide database, which links to related information such as taxonomy, genomes, protein sequences and structures, and biomedical journal literature in PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. Recent updates include changes to sequence identifiers, submission wizards for 16S and Influenza sequences, and an Identical Protein Groups resource.
doi:10.1093/nar/gkx1094 pmid:29140468 pmcid:PMC5753231 fatcat:tcapoinydngldd7erbnmv3x2aq

GenBank

Eric W Sayers, Mark Cavanaugh, Karen Clark, Kim D Pruitt, Conrad L Schoch, Stephen T Sherry, Ilene Karsch-Mizrachi
2021 Nucleic Acids Research  
GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 15.3 trillion base pairs from over 2.5 billion nucleotide sequences for 504 000 formally described species. Recent updates include resources for data from the SARS-CoV-2 virus, including a SARS-CoV-2 landing page, NCBI Datasets, NCBI Virus and the Submission Portal. We also discuss upcoming changes to GI identifiers, a new data management interface for BioProject, and advice for providing contextual metadata in submissions.
doi:10.1093/nar/gkab1135 pmid:34850943 pmcid:PMC8690257 fatcat:bgeuokddybcwnjh3mpy7rah6rm

Solution Conformations of a Trimannoside from Nuclear Magnetic Resonance and Molecular Dynamics Simulations

Eric W. Sayers, James H. Prestegard
2000 Biophysical Journal  
N-linked oligosaccharides often act as ligands for receptor proteins in a variety of cell recognition processes. Knowledge of the solution conformations, as well as protein-bound conformations, of these oligosaccharides is required to understand these important interactions. In this paper we present a model for the solution conformations sampled by a simple trimannoside, methyl 3,6-di-O-(␣-D-mannopyranosyl)-␣-D-mannopyranoside, which contains two of the most commonly found glycosidic linkages
more » ... N-linked oligosaccharides. This model was derived from simulated annealing protocols incorporating distance restraints extracted from NOESY spectra along with torsional restraints computed from three-bond 1 H-13 C coupling constants measured across the glycosidic bonds. The model was refined in light of unrestrained molecular dynamics simulations conducted in the presence of solvent water. The resulting model depicts a molecule undergoing conformational averaging in solution, adopting four major and two minor conformations. The four major conformations arise from a pair of two-state transitions, one each at the ␣(133) and ␣(136) linkages, whereas the minor conformations result from an additional transition of the ␣(136) linkage. Our data also suggest that the ␣(133) transition is fast and changes the molecular shape slightly, whereas the ␣(136) is much slower and alters the molecular shape dramatically.
doi:10.1016/s0006-3495(00)76563-5 pmid:11106634 pmcid:PMC1301205 fatcat:y3gfhj3tebdkznsf33tq47bnke

Alison Jane Graham Bell Antony Robert Phillips Ellis Enid Josephine Fair Robert Charles Hunt Ernst Jacoby David Kendall Eric Clare ("Ric") Raybould Denis George Blackwood Richards Matthew Herbert Patrick Sayers Ruth Janet Smith David Spencer Andrew Felix Verney

R W Hughes
2000 BMJ (Clinical Research Edition)  
[E W Borastero] [J R Tighe] Matthew Herbert Patrick SayersDirector of army pathology, 1964-7 (b Croydon 1908 q St Thomas's 1932; MD, FRCPath; OBE), d 12 January 2000.  ... 
doi:10.1136/bmj.320.7240.1012 pmid:10753168 pmcid:PMC1117883 fatcat:qvsnd7wptnaezndpo3bdohvoty

Conformation of a Trimannoside Bound to Mannose-Binding Protein by Nuclear Magnetic Resonance and Molecular Dynamics Simulations

Eric W. Sayers, James H. Prestegard
2002 Biophysical Journal  
Two-dimensional (2D) 1 H-13 C HSQC spectra were recorded at 35°C on the Omega 500 as described previously (Sayers et al., 1998) .  ...  Preparation of MBP-2 The purification of MBP-2 was performed as described previously (Weis et al., 1991a; Sayers et al., 1998) with the following modifications.  ... 
doi:10.1016/s0006-3495(02)75610-5 pmid:11964255 pmcid:PMC1302057 fatcat:njwdqiii3fafvjhrex3qdjebqy

BLAST: a more efficient report with usability improvements

Grzegorz M. Boratyn, Christiam Camacho, Peter S. Cooper, George Coulouris, Amelia Fong, Ning Ma, Thomas L. Madden, Wayne T. Matten, Scott D. McGinnis, Yuri Merezhuk, Yan Raytselis, Eric W. Sayers (+3 others)
2013 Nucleic Acids Research  
The Basic Local Alignment Search Tool (BLAST) website at the National Center for Biotechnology (NCBI) is an important resource for searching and aligning sequences. A new BLAST report allows faster loading of alignments, adds navigation aids, allows easy downloading of subject sequences and reports and has improved usability. Here, we describe these improvements to the BLAST report, discuss design decisions, describe other improvements to the search page and database documentation and outline
more » ... ans for future development. The NCBI BLAST URL is http://blast.ncbi.nlm.nih.gov.
doi:10.1093/nar/gkt282 pmid:23609542 pmcid:PMC3692093 fatcat:ba32l5nfyjarrbjpewzuaybvei

Direct correlation between potentiometric and impedance biosensing of antibody-antigen interactions using an integrated system

Meng-Yen Tsai, Niamh Creedon, Eleanor Brightbill, Spyridon Pavlidis, Billyde Brown, Darren W. Gray, Niall Shields, Ríona Sayers, Mark H. Mooney, Alan O'Riordan, Eric M. Vogel
2017 Applied Physics Letters  
Au micro-strip WE in 22 conventional Randle circuit model comprises of series resistance (Rs), surface capacitance (Csurface usually 1 modeled using constant phase elements, CPE), Warburg resistance (W)  ...  working electrode decreases, the diffusion layer thickness decreases, 3 and the current is less dependent on the diffusion of reacting species toward the WE. 16 As a result, the 4 mass transfer dominated W  ... 
doi:10.1063/1.4986190 fatcat:ywgf7r4bi5cw7g3evacoe63xgm

Database resources of the National Center for Biotechnology Information

Eric W Sayers, Jeffrey Beck, Evan E Bolton, Devon Bourexis, James R Brister, Kathi Canese, Donald C Comeau, Kathryn Funk, Sunghwan Kim, William Klimke, Aron Marchler-Bauer, Melissa Landrum (+13 others)
2020 Nucleic Acids Research  
screening studies BioSystems 983 968 molecular pathways with links to genes, proteins and chemicals * To whom correspondence should be addressed.Tel: +1 301 496 2475, Fax: +1 301 480 9241; Email: sayers  ... 
doi:10.1093/nar/gkaa892 pmid:33095870 fatcat:pptmq2emtjft7e62jnnm62t6ny
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