Search software

The National Chemical Laboratory for Industry (NCLl), Japan, has developed an integrated Spectral Database System (SDBS) which is available to users in Japan. AU spectra were deterrnined at NCLl under controUed conditions and are available on a PC/CD-ROM or magnetic tape. The system has both H-nmr (6000 compounds) and C-nmr spectra (5700 compounds), along with searching software. NCLl has also developed an integrated C— H-nmr system that can be used for two-dimensional data elucidation (70,71). 

A computer file of about 19,000 peak wavenumbers and intensities, along with search software, is distributed by the Infrared Data Committee of Japan (IRDC). Donated spectra, which are evaluated by the Coblentz Society in coUaboration with the Joint Committee on Atomic and Molecular Physical Data (JCAMP), are digitized and made avaUable (64). Almost 25,000 ir spectra are avaUable on the SDBS system developed by the NCLl as described. A project was initiated at the University of California, Riverside, in 1986 for the constmction of a database of digitized ftir spectra. The team involved also developed algorithms for spectra evaluation (75). Other sources of spectral Hbraries include Sprouse Scientific, Aston Scientific, and the American Society for Testing and Materials (ASTM). 

Eraser WiUiams (Scientific Systems Ltd.) 1 Qr- r-nmr PC-based PC-SABRE search software... 

Sadder Laboratories 13 C-nmr, ir. 30,000 60,000 PC-based PPC search software substmcture... 

Full-Text Patent Databases. The LEXPAT database on the LEXIS— NEXIS system, the first commercially available full-text patent file, receives its greatest use from patent attorneys and has been relatively unused by other patent information speciaUsts. This may be attributed to search software that is quite different from the type familiar to information speciaUsts, no matter what their preferred host system. This situation has changed with dialog s release of the PATEULL files followed by STN s USPATEULL, both searchable by familiar Boolean techniques and featuring greater... 

Reliable quantification is based on peak-search software that combines peak location, peak identification, and element deduction. Element deduction means that, for unambiguous detection, at least two of the principal peaks must be detected for each analyte of interest. In trace analysis, only the strongest peaks can be detected and special attention must be paid to interfering satellites and spurious peaks. 

How does one go about finding all of the relevant proteins in a database once it has been decided to carry out an analysis of an entire protein family The simplest approach is to use similarity search software such as SSEARCH or FASTA (Smith and Waterman, 1981 Pearson and Lipman, 1988) or BLAST (Altschul et al, 1997) with the amino acid sequences of one or two well-known members of the family as queries. The problem is initially the same as that of identifying all proteins that are homologous to a family of proteins, although with some important practical differ-... 

Another resource derived from BLOCKS and PRINTS is IDENTIFY, which, instead of encoding the exact information at each position in an alignment, tolerates alternative residues according to a set of prescribed groupings of related biochemical properties. IDENTIFY and its search software, eMOTIF (Huang and Brutlag, 2001), are accessible for use from the protein function Web server of the Biochemistry Department at Stanford University, http //dna.Stanford.edu/identify/. PANAL (http //mgd.ahc.umn.edu/panal/run panal.html) of Computational Biology Centers at the University of Minnesota is a combined resource for ProSite, BLOCKS, PRINTS, and Pfam (Bateman et al., 2000). 

Standard and chemical Office software. Databases for the storage and retrieval of information generated in the laboratory, with search software. Document management LIMS. Online searching of external databases, catalogues and other information. Electronic Notebooks. Knowledge Management. 

Searching the spectrum of an unknown chemical against a spectral library is a routine method used to identify chemicals. Most of the commercial infrared instruments include library search software that has several search algorithms to choose from. The search algorithm can sometimes have a strong effect on the library search result. This is due to the different ways the actual comparison between the spectra is done. Especially when the library and the unknown spectra have been measured differently (e.g. using solid KBr disk and cryodeposition GC/FTIR), the... 

The inorganic equivalent of the CSD is the Inorganic Crystal Structure Database (ICSD) (FIZ 2001 Bergerhoff et al. 1983). This currently contains over 53000 entries (August 2000) with two updates per year, and may be searched in a manner similar to that used for the CSD. There are currently efforts under way to unify the searching software for these two important data bases, a move which would considerably facilitate and widen their use. Another useful source is the inorganic section of the PDF (ICDD 2001 Jenkins and Snyder 1996). For older references, the first two volumes of Groth (1906, 1908) are particularly valuable. 

Sadtler Molecular Structure Search Software Bio-Rad, Sadtler Division Sadtler Research Laboratories 3316 Spring Garden Street Philadelphia, PA 19104, U.S.A. 

Figure 9.13. Example 2D substructure search queries with various atom and bond query features. The more features that are present, the more flexible the search becomes, but the search may also require more time to complete. There is a trade-off between putting the flexibility into the database (i.e., storing and indexing multiple forms of a structure) and putting the flexibility into the search query and the search software.

Sample preparation for XRD is rapid and data is acquired by a computer which also controls the sample changer. A typical acquisition time would be a few hours. For routine operations, such as determining zeolite lattice parameters, it is also possible to process data automatically. Phase identification, aided by a JCPDS database search software, takes a few tens of minutes. 

Schug, J. and Overton, G. C. (1997) TESS Transcription Element Search Software on the WWW. University of Pennsylvania, Philadelphia, PA. 

D. L. Hansen, The Spouse Collection of Spectra. I. Polymers, II. Solvents by Cylindrical Internal Reflectance, III. Surface Active Agents, TV. Common Solvents—Condensed Phase, Vapor Phase and Mass Spectra. Amsterdam Elsevier Science, 1987-1988. Peak table search software available for each. 

The Wiley/NIST Registry of Mass Spectral Data, 7th edition, 1999, contains over 390,000 reference spectra ThftRegistry has 32-bit search software to identify unknown mass spectra. You can view reference spectra by mass, molecular weight, or peaks. 

In databases built using bottom-up approaches, any computational representation believed to be common to all members of a particular domain family can be used. This representation, in conjunction with appropriate searching software, should optimally be able to distinguish all true family members from the background noise of unrelated proteins stored in sequence databases. This is a challenging problem, tackled with varying degrees of sophistication by different approaches. At the most basic level, the representation can consist of a simple pattern of amino acids common to a particular domain. Such an approach is found in... 

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