Database searching technique

Pairs of similar reads are identified using a fast database search technique. Letfi,f2,... be all the input reads in given orientation and let rx be the reverse complement of read fx. The goal of this step is to find quickly pairs of similar reads fx and fy with x < y and pairs of similar reads rx and fY with x [Pg.468]

Improtantly, there are several highly specific and useful database searching techniques have been duly introdueed into a plethora of most recent database searching system, namely ... 

The reaction database compiled on Biochemical Pathways can be accessed on the web and can be investigated with the retrieval system C ROL (Compound Access and Retrieval On Line) [211 that provides a variety of powerful search techniques. The Biochemical Pathways database is split into a database of chemical structures and a database of chemical reactions that can be searched independently but which have been provided with efficient crosslinks between these two databases. 

Another technique employs a database search. The calculation starts with a molecular structure and searches a database of known spectra to find those with the most similar molecular structure. The known spectra are then used to derive parameters for inclusion in a group additivity calculation. This can be a fairly sophisticated technique incorporating weight factors to account for how closely the known molecule conforms to typical values for the component functional groups. The use of a large database of compounds can make this a very accurate technique. It also ensures that liquid, rather than gas-phase, spectra are being predicted. 

Database searches can be used to find a reference to a known compound with a matching substructure. This is a particularly good technique if a portion of the molecule has an unusual structure. It may indicate a synthesis route or simply identify a likely starting material. 

Secondary sources of patent information, Advances in patent documentation. Types of patent information searches. On-line database searching methods. Cross-file and multifile techniques. 

Form of Data. Databases can be classified in many ways. One method is by form of data representation, ie, data may be in the form of words, numbers, images, or sounds. The corresponding databases may then be considered to be word-oriented, number-oriented, image-oriented (video), or sound-oriented (audio). Data representation affects file stmctures and software for search and data retrieval. Thus the stmctures and search techniques vary considerably among these four basic classes. Table 1 gives databases as classified by form of data representation. 

Bures, M. G., Searching Techniques for Databases of Three-Dimensional Chemical Structures, 21, 467. 

In this case, systematic methods for generation of feasible molecular and mixture candidates have been reported for the design of functional chemical products [see Achenie et al (2003)]. Methods based on database search, total enumeration of feasible candidates (rule-based techniques that avoid a combinatorial explosion), mathematical programming, genetic algorithm, and,... 

The standard screening approach when several active molecules have been identified is pharmacophore mapping followed by 3D database searching. This approach assumes that the active molecules have a common mode of action and that features that are common to all of the molecules describe the pharmacophoric pattern responsible for the observed bioactivity. This is a powerful technique but one that may not be applicable to the structurally heterogeneous hits that characterize typical HTS experiments or sets of competitor compounds drawn from the public literature. In such cases, it is appropriate to consider approaches based on 2D similarity searching and we present here a comparison of approaches for combining the structural information that can be gleaned from a small set of reference structures. 

This is a rapidly developing subject. There is an increasing number of on-line databases readily available to the organic chemist. It is likely that all organic chemists will require skills to conduct searches of such databases in future. Any advanced course in organic chemistry should therefore provide an introduction to on-line searching techniques in order to provide the basis for development later in the student s career. A detailed account of this field is beyond the scope of this appendix and would in any case date rapidly. The reader is referred to recent monographs for further information.4,7... 

The development and use of various protein sequence databases for automated search routines (Eng et al., 1994 Clauser et al., 1999) are an essential component of protein analysis that uses mass spectrometry techniques. These programs (i.e., SEQUEST, MASCOT) require only a few peptides for matching therefore, the absence of a match for a particular peptide does not affect the search performance. Using protein database searches provides an efficient way of confirming a putative sequence from corresponding full-scan mass spectrometry and MS/MS data. 

---