Translatability database

The JME can also serve as a query input tool for structure databases by allowing creation of complex substructure queries (Figure 2-130), which are automatically translated into SMARTS [22]. With the help of simple HTML-format elements the creation of 3D structure queries is also possible, as were used in the 3D pharmacophore searches in the NCI database system [129]. Creation of reac-... 

Any attempt in learning also needs information on situations where the event to be studied will not occur. This principle, if translated to learning on reactions, would require information on reactions that will not proceed. Unfortunately, such information is not contained in reaction databases, and therefore has to he generated. In our case, we also needed information on which regioisomer is not formed, or is formed only to a minor extent, in a pyrazole synthesis. 

Swiss-Prot, TrEMBL Annotated non-redundant protein sequence database, TrEMBL is a computer-annotated supplement to Swiss-Prot. TrEMBL contains the translations of all coding sequences present in the EMBL Nucleotide Sequence Database which are no yet integrated into Swiss-Prot... 

Risk and uncertainty associated with each venture should translate, ia theory, iato a minimum acceptable net return rate for that venture. Whereas this translation is often accompHshed implicitly by an experienced manager, any formal procedure suffers from the lack of an equation relating the NRR to risk, as well as the lack of suitable risk data. A weaker alternative is the selection of a minimum acceptable net return rate averaged for a class of proposed ventures. The needed database, from a collection of previous process ventures, consists of NPV, iavestment, venture life, inflation, process novelty, decision (acceptance or rejection), and result data. 

As computing capabiUty has improved, the need for automated methods of determining connectivity indexes, as well as group compositions and other stmctural parameters, for existing databases of chemical species has increased in importance. New naming techniques, such as SMILES, have been proposed which can be easily translated to these indexes and parameters by computer algorithms. Discussions of the more recent work in this area are available (281,282). SMILES has been used to input Contaminant stmctures into an expert system for aquatic toxicity prediction by generating LSER parameter values (243,258). 

The presence of errors within the underlying database fudher degrades the accuracy and precision of the parameter e.stimate. If the database contains bias, this will translate into bias in the parameter estimates. In the flash example referenced above, including reasonable database uncertainty in the phase equilibria increases me 95 percent confidence interval to 14. As the database uncertainty increases, the uncertainty in the resultant parameter estimate increases as shown by the trend line represented in Fig. 30-24. Failure to account for the database uncertainty results in poor extrapolations to other operating conditions. 

Raw data is almost always incomplete, being highly dependent on the data production platform and often localized to a platform or regional database. Applications (and processes) generate data. However, applications often use proprietary data types and cannot parse data types from other third-party applications. It is important to consider that there are translation issues plus the host of reasons stated below in the requirements for data standards. 

Translation and forwarding - converting submitted documents into formats that will load to EPA databases, and forwarding them to the appropriate systems. 

The QCRNA database is viewable and searchable with a web browser on the internet and it is also contained as a MySQL database that is easily incorporated with parameter optimization software to allow for the rapid development of specific reaction parameters. Molecular structures can be viewed with the JMOL [47, 48] or MOLDEN [49, 50] programs as viewers for chemical MIME types. If the web browser is JAVA-enabled, then the JMOL software will automatically load as a web applet. Both programs allow the structure to be manipulated, i.e., rotated, scaled, and translated, and allow for measurement of internal coordinates, e.g., bond lengths, angles, and dihedral angles. Similarly, animations of the vibrational frequencies are available and can be viewed with either program. 

Demirev, P. A. Lin, J. S. Pineda, F. J. Fenselau, C. Bioinformatics and mass spectrometry for microorganism identification Proteome-wide post-translational modifications and database search algorithms for characterization of intact H. Pylori. Anal. Chem. 2001, 73, 4566 573. 

MS instruments measure the mass-to-charge ratio (m/z) values of the smallest of molecules very accurately. In addition, the development of translated genomic databases and specialized software algorithms that rapidly search MS data against theoretical spectra of known or predicted proteins within databases is an important component that greatly facilitated the emergence of mass spectrometry-based proteomics as a key approach for large-scale proteomic analysis.15... 

TrEMBL (http //www.expasy.org/sprot), database of the European Bioinformatics Institute, translated EMBL. Generated by computer translation of genetic information from the EMBL database. Automatically annotated. 

In using a relational database, the interlinked object structure is translated into a representation based on tables and rows. Each object typically is a row in a table one table is defined for each class (sans inheritance). 

Various verification steps have been introduced to ensure that SPTR is comprehensive and contains all relevant data sources. The main source of new protein sequences is the translations of CDS in the nucleotide sequence databases. The up-to-date inclusion of new protein sequence entries is ensured by the weekly translation of EMBL-NEW (the updates to the EMBL nucleotide sequence database). The three collaborating nucleotide sequence databases DDBJ, EMBL, and GenBank exchange their data on a daily basis. Therefore any protein coding sequence submitted to DDBJ/EMBL/GenBank will appear in SPTR within 2 weeks in the worst case and within less than 1 week in the average case. 

It is only natural that, to date, bioinformatics tools contribute most to the analysis of amino acid sequences. Only a small amount of current sequence data is subjected to direct experimentation. The majority of amino acid sequences currently accessible in public databases have been derived by in silico translations of nucleic acid sequence data, despite the fact that amino acid sequencing was introduced historically long before nucleic acid sequencing. It is hard to predict the future of the experimental generation of primary data. Certainly, sequencing of nucleic acids continues to become cheaper and faster, and novel techniques may further enhance the production of data. DNA chips are already used to detect differences between very similar sequences other methods may generate DNA data even more efficiently. 

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