Computer search string

In all our discussion of computer searching so far, we have really only been concerned with establishing within a search file the existence of certain specified character strings. However, if we go back to our chemist doing his manual searching we will realise that it is not merely the occurrence of particular key words which "triggers him off" he also takes into account their context. For instance he may be very interested in the ultraviolet spectra of unsaturated ketones but not at all interested in their infrared spectra. The mere occurrence of suitable chemical names will not alone be enough to arouse his interest. 

In the earliest days of on-line databases, all three indexing types coUapsed into the third. Using older manual tools, it was difficult to coordinate more than two or three concepts, but the computer made that easier. Each concept in a search can be represented by a string of synonyms or alternatives, and searching can be done for two such parameters or more. Thus, Boolean logic expressions can easily be constmcted as follows ... 

XuE, L, Godden, J., and Bajorath, J. Database searching for compounds with similar biological activity using short binary bit string representations of molecules./. Chem. Inf. Comput. Sci. 1999, 39(5), 881-886. 

A sequence alignment is a way of determining the similarity between two strings. This is a classical question in computer science, and has an exact solution referred to as the Smith/Waterman alignment. Unfortunately, this exact solution can be slow when analyzing large sequences, and therefore, approximate methods, such as Basic Local Alignment Search Tool (BLAST), have been developed to identify very similar sequences. 

EMBL Nucleotide Sequence Database. SWISS-PROT consists of core sequence data with minimal redundancy, citation and extensive annotations including protein function, post-translational modifications, domain sites, protein structural information, diseases associated with protein deficiencies and variants. SWISS-PROT and TrEMBL are available at EBI site, http //www.ebi.ac.uk/swissprot/, and ExPASy site, http //www.expasy.ch/sprot/. From the SWISS-PROT and TrEMBL page of ExPASy site, click Full text search (under Access to SWISS-PROT and TrEMBL) to open the search page (Figure 11.3). Enter the keyword string (use Boolean expression if required), check SWISS-PROT box, and click the Submit button. Select the desired entry from the returned list to view the annotated sequence data in Swiss-Prot format. An output in the fasta format can be requested. Links to BLAST, feature table, some ExPASy proteomic tools (e.g., Compute pI/Mw, ProtParam, ProfileScan, ProtScale, PeptideMass, ScanProsite), and structure (SWISS-MODEL) are provided on the page. 

Table A.4 shows commonly used fragment keys the MACCS publicl66-keys. This table is used with the publicl66keys function above to produce a bit string key for use in filtering before substructure searching and for similarity computations. The table consists of SMARTS patterns3 used to identify each of 166 substructures.

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