The book chapter introduces the National Center for Biotechnology Information (NCBI) Genome Workbench, a desktop GUI software package to manipulate and visualize complex molecular biology models ...provided in many data formats. Genome Workbench integrates graphical views and computational tools in a single package to facilitate discoveries. In this chapter we provide a step-by-step protocol guidance on how to do comparative analysis of sequences using NCBI BLAST and multiple sequence alignment algorithms, build phylogenetic trees, and use graphical views for sequences, alignments, and trees to validate the findings. The software package can be used to prepare high-quality whole genome submissions to NCBI. The software package is user-friendly and includes validation and editing tools to fix errors as part of preparing the submission.
Abstract
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database ...and the PubMed database of citations and abstracts published in life science journals. The Entrez system provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Custom implementations of the BLAST program provide sequence-based searching of many specialized datasets. New resources released in the past year include a new PubMed interface, a sequence database search and a gene orthologs page. Additional resources that were updated in the past year include PMC, Bookshelf, My Bibliography, Assembly, RefSeq, viral genomes, the prokaryotic genome annotation pipeline, Genome Workbench, dbSNP, BLAST, Primer-BLAST, IgBLAST and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
The National Center for Biotechnology Information (NCBI) is an archive providing free access to a wide range and large volume of biological sequence data and literature. Staff scientists at NCBI ...analyze user-submitted data in the archive, producing gene and SNP annotation and generating sequence alignment tools. NCBI's flagship genome browser, Genome Data Viewer (GDV), displays our in-house RefSeq annotation; is integrated with other NCBI resources such as Gene, dbGaP, and BLAST; and provides a platform for customized analysis and visualization. Here, we describe how members of the biomedical research community can use GDV and the related NCBI Sequence Viewer (SV) to access, analyze, and disseminate NCBI and custom biomedical sequence data. In addition, we report how users can add SV to their own web pages to create a custom graphical sequence display without the need for infrastructure investments or back-end deployments.
A multitude of metrics exist to assign scores to synthetic routes within computer-aided synthesis planning (CASP) tools. A quantitative scoring method is necessary to identify the most promising ...synthetic approaches to a molecule. However, current CASP tools are limited in their capacity to evaluate reaction selectivity and are unable to fully account for the effect of side products on the purification sequences associated with chemical syntheses. We develop a novel quantitative metric called ExtractionScore for evaluating synthetic routes based on the predicted identities of side products as well as the separability of major and side products by liquid–liquid extraction based on chemical property prediction. By comparing industrially practiced routes to a collection of 200 pharmaceutically relevant compounds with routes suggested by state-of-the-art CASP software, we show that ExtractionScore may improve retrosynthetic recommendations by incorporating information about the formation of side products.
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•Wind power for local energy supply and to make ammonia as fertilizer and fuel.•Emissions eliminated at annual net present cost of dollar17.60/tonCO2.•Revenue from consistent and ...predictable power sale to grid in October through May.•Optimal design uses both ammonia and hydrogen as energy storage media.
This work presents a new vision for sustainable energy supply and agriculture: an ammonia-based sustainable energy agriculture (ABSEA) system. This intensified system uses renewables to produce ammonia both as fertilizer and as fuel for tractors and grain drying, to meet local electrical power demand and to provide predictable, consistent power export to the grid. The conceptual design of this system exploits synergies between ammonia production and energy supply to allow for economic viability, specifically time-varying chemical production as well as the potential of ammonia and hydrogen as energy storage media. A framework for combined optimization of the ABSEA design and its inherently time-varying operating schedule is proposed with a view on further improving economic competitiveness. A case study which considers the use of wind turbines to meet ammonia fertilizer and fuel demands of 40,300 kg/year and an annual hourly average power demand of 985 kW demonstrates the promise of the ABSEA system and the associated design-scheduling optimization framework. The annual net present cost is approximately $75,000, which corresponds to an emissions reduction cost of $17.60/tonCO2. The ABSEA optimal design uses both hydrogen and ammonia, but not a battery, for energy storage, illustrating their efficacy in this synergistic application.
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and ...the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (PubMed Central (PMC), Bookshelf and PubReader), health (ClinVar, dbGaP, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen), genomes (BioProject, Assembly, Genome, BioSample, dbSNP, dbVar, Epigenomics, the Map Viewer, Nucleotide, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser and the Trace Archive), genes (Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and chemicals (Biosystems and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for most of these databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank
nucleic acid sequence database and the ...PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 37 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the past year include iCn3D, MutaBind, and the Antimicrobial Resistance Gene Reference Database; and resources that were updated in the past year include My Bibliography, SciENcv, the Pathogen Detection Project, Assembly, Genome, the Genome Data Viewer, BLAST and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
Catalytic enhancement of chemical reactions
via
heterogeneous materials occurs through stabilization of transition states at designed active sites, but dramatically greater rate acceleration on that ...same active site can be achieved when the surface intermediates oscillate in binding energy. The applied oscillation amplitude and frequency can accelerate reactions orders of magnitude above the catalytic rates of static systems, provided the active site dynamics are tuned to the natural frequencies of the surface chemistry. In this work, differences in the characteristics of parallel reactions are exploited
via
selective application of active site dynamics (0 < Δ
U
< 1.0 eV amplitude, 10
−6
<
f
< 10
4
Hz frequency) to control the extent of competing reactions occurring on the shared catalytic surface. Simulation of multiple parallel reaction systems with broad range of variation in chemical parameters revealed that parallel chemistries are highly tunable in selectivity between either pure product, even when specific products are not selectively produced under static conditions. Two mechanisms leading to dynamic selectivity control were identified: (i) surface thermodynamic control of one product species under strong binding conditions, or (ii) catalytic resonance of the kinetics of one reaction over the other. These dynamic parallel pathway control strategies applied to a host of simulated chemical conditions indicate significant potential for improving the catalytic performance of many important industrial chemical reactions beyond their existing static performance.
Branched catalytic reaction networks with oscillating chemical pathways perfectly select for reaction products at varying frequency.
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