scholarly journals GenBank

2020 ◽  
Vol 49 (D1) ◽  
pp. D92-D96
Author(s):  
Eric W Sayers ◽  
Mark Cavanaugh ◽  
Karen Clark ◽  
Kim D Pruitt ◽  
Conrad L Schoch ◽  
...  
Keyword(s):  
Data Exchange ◽  
Data Bank ◽  
Nucleotide Sequences ◽  
Public Database ◽  
Base Pairs ◽  
Daily Data ◽  
European Nucleotide Archive ◽  
Bank Of Japan

Abstract 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 viruses, new taxonomy queries for viruses and prokaryotes, and simplified submission processes for EST and GSS sequences.

scholarly journals GenBank

2019 ◽  
Author(s):  
Eric W Sayers ◽  
Mark Cavanaugh ◽  
Karen Clark ◽  
James Ostell ◽  
Kim D Pruitt ◽  
...  
Keyword(s):  
Data Exchange ◽  
Data Bank ◽  
Nucleotide Sequences ◽  
Public Database ◽  
Base Pairs ◽  
Viral Genomes ◽  
Daily Data ◽  
European Nucleotide Archive ◽  
Bank Of Japan

Abstract GenBank® (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains over 6.25 trillion base pairs from over 1.6 billion nucleotide sequences for 450 000 formally described species. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. Recent updates include a new version of Genome Workbench that supports GenBank submissions, new submission wizards for viral genomes, enhancements to BankIt and improved handling of taxonomy for sequences from pathogens.

New Record of Macrobrachium lar (Fabricius, 1798) (Crustacea: Decapoda: Palaemonidae) from Al-Hammar Marsh, Southern Iraq

2021 ◽  
Vol 5 (1) ◽  
pp. 33-43
Author(s):  
Abdul-Hussein Ghazi
Keyword(s):  
Dna Sequences ◽  
Brackish Water ◽  
New Record ◽  
Data Bank ◽  
Morphological Features ◽  
Freshwater Prawn ◽  
Dna Analyses ◽  
European Nucleotide Archive ◽  
Bank Of Japan ◽  
Southern Iraq

A species of freshwater prawn Macrobrachium was newly recorded from Al-Hammar marsh, Southern Iraq. Morphological features accompanied by 18 S r DNA analyses indicated that the species is Macrobrachum lar. DNA sequences of specimens of this species from the marsh is deposited at the GenBank for DNA as a new global isolate and was published by The National Center for Biotechnology Information (NCBI), the European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ). M. lar inhabit deep sections of streams and brackish water, adults live in freshwater, while juveniles can be found in brackish or saltwater, the total length of M. lar recorded in this study was ranged between 72 and 109 mm for males and between 61 and 93 mm for females.

scholarly journals Extension of the sasCIF format and its applications for data processing and deposition

2016 ◽  
Vol 49 (1) ◽  
pp. 302-310 ◽  
Author(s):  
Michael Kachala ◽  
John Westbrook ◽  
Dmitri Svergun
Keyword(s):  
Data Analysis ◽  
Data Processing ◽  
Data Exchange ◽  
Hybrid Methods ◽  
Data Bank ◽  
Relevant Information ◽  
Experimental Information ◽  
Biological Data ◽  
Task Forces ◽  
Software Modules

Recent advances in small-angle scattering (SAS) experimental facilities and data analysis methods have prompted a dramatic increase in the number of users and of projects conducted, causing an upsurge in the number of objects studied, experimental data available and structural models generated. To organize the data and models and make them accessible to the community, the Task Forces on SAS and hybrid methods for the International Union of Crystallography and the Worldwide Protein Data Bank envisage developing a federated approach to SAS data and model archiving. Within the framework of this approach, the existing databases may exchange information and provide independent but synchronized entries to users. At present, ways of exchanging information between the various SAS databases are not established, leading to possible duplication and incompatibility of entries, and limiting the opportunities for data-driven research for SAS users. In this work, a solution is developed to resolve these issues and provide a universal exchange format for the community, based on the use of the widely adopted crystallographic information framework (CIF). The previous version of the sasCIF format, implemented as an extension of the core CIF dictionary, has been available since 2000 to facilitate SAS data exchange between laboratories. The sasCIF format has now been extended to describe comprehensively the necessary experimental information, results and models, including relevant metadata for SAS data analysis and for deposition into a database. Processing tools for these files (sasCIFtools) have been developed, and these are available both as standalone open-source programs and integrated into the SAS Biological Data Bank, allowing the export and import of data entries as sasCIF files. Software modules to save the relevant information directly from beamline data-processing pipelines in sasCIF format are also developed. This update of sasCIF and the relevant tools are an important step in the standardization of the way SAS data are presented and exchanged, to make the results easily accessible to users and to promote further the application of SAS in the structural biology community.

scholarly journals Accurate geometrical restraints for Watson–Crick base pairs

2019 ◽  
Vol 75 (2) ◽  
pp. 235-245 ◽  
Author(s):  
Miroslaw Gilski ◽  
Jianbo Zhao ◽  
Marcin Kowiel ◽  
Dariusz Brzezinski ◽  
Douglas H. Turner ◽  
...  
Keyword(s):  
Structural Information ◽  
Data Bank ◽  
Base Pairs ◽  
Acta Cryst ◽  
Ultrahigh Resolution ◽  
Cryo Electron Microscopy ◽  
Structural Database ◽  
Different Sources ◽  
Best Parameters

Geometrical restraints provide key structural information for the determination of biomolecular structures at lower resolution by experimental methods such as crystallography or cryo-electron microscopy. In this work, restraint targets for nucleic acids bases are derived from three different sources and compared: small-molecule crystal structures in the Cambridge Structural Database (CSD), ultrahigh-resolution structures in the Protein Data Bank (PDB) and quantum-mechanical (QM) calculations. The best parameters are those based on CSD structures. After over two decades, the standard library of Parkinson et al. [(1996), Acta Cryst. D52, 57–64] is still valid, but improvements are possible with the use of the current CSD database. The CSD-derived geometry is fully compatible with Watson–Crick base pairs, as comparisons with QM results for isolated and paired bases clearly show that the CSD targets closely correspond to proper base pairing. While the QM results are capable of distinguishing between single and paired bases, their level of accuracy is, on average, nearly two times lower than for the CSD-derived targets when gauged by root-mean-square deviations from ultrahigh-resolution structures in the PDB. Nevertheless, the accuracy of QM results appears sufficient to provide stereochemical targets for synthetic base pairs where no reliable experimental structural information is available. To enable future tests for this approach, QM calculations are provided for isocytosine, isoguanine and the iCiG base pair.

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