Abstract—Bioinformatics and Cheminformatics use computer as disciplines providing tools for acquisition, storage, processing, analysis, integrate data and for the development of potential applications of biological and chemical data. A chemical database is one of the databases that exclusively designed to store chemical information. NMRShiftDB is one of the main databases that used to represent the chemical structures in 2D or 3D structures. SMILES format is one of many ways to write a chemical structure in a linear format. In this study we extracted Antimicrobial Structures in SMILES format from NMRShiftDB and stored it in our Local Data Warehouse with its corresponding information. Additionally, we developed a searching tool that would response to user’s query using the JME Editor tool that allows user to draw or edit molecules and converts the drawn structure into SMILES format. We applied Quick Search algorithm to search for Antimicrobial Structures in our Local Data Ware House. Keywords—Exact String-matching Algorithms; NMRShiftDB; SMILES Format; Antimicrobial Structures. I. INTRODUCTION IOINFORMATICS has been regarded widely as a key discipline for the scientific development and it has a big amount of unlimited increasing and distributed information [1]. Bioinformatics has several categories included computational biology, computer science relating to biology, management of bioinformatics infrastructure and so forth [16]. Cheminformatics is the applying of computer and informational techniques with problems in the field of chemistry for the intended purpose of making better and fast decisions in the area of drug and chemical compounds [10]. Computational biology and chemistry that use computational methods handle large amount of data, so biologists can pinpoint genes, DNA or proteins and chemists can pinpoint chemical structures. Manuscript received June 30, 2007. This work was supported by the Government of Malaysia - Ministry of Science, Technology and Innovation (MOSTI) under E-Science Grant no 01-01-05-5F0182. Ahmad Fadel Klaib is Master Student at the School Computer Sciences, USM, Malaysia (e-mail: ahmadklaib@yahoo.com). Zurinahni Zainol and Wahidah Hussin are Senior Lecturer at the School Computer Sciences, USM, Malaysia (e-mail: zuri@cs.usm.my, wahidah@cs.usm.my). Nurul Hashimah Ahamed is Research Officer at the School Computer Sciences, USM, Malaysia (e-mail: nurul@cs.usm.my). Rosma Ahmad is Senior Lecturer at the School Industrial Technology, USM, Malaysia (e-mail: rosmah@usm.my). NMRShiftDB is a web database for organic structures and their nuclear magnetic resonance spectra [4, 13]. It is an open- source, open-access application and allows for spectrum prediction as well as for searching spectra, structures and other properties. Chemical structures are represented using lines representing chemical bonds between atoms and shaped on 2D structural formulae. SMILES format is one of many ways to write a chemical structure in a linear format [18]. Linear formulas have an advantage over graphical structures because they are easily read through computer code and computational use, especially for search and storage [19]. SMILES format contains the same information as might be found in an extended connection table. The primary reason SMILES is more useful than a connection table is that it is a linguistic construct, rather than a computer data structure. There are popular kinds of existing structures called Antimicrobial Structures [11] which have been shown to be effective in experimental infections with multi drugs as a substance that kills or inhibits the growth of microbes such as bacteria (antibacterial activity), fungi (antifungal activity) and viruses (antiviral activity) [20]. Thus our research aimed to help biologists and chemists by extracting Antimicrobial Structures from NMRShiftDB and allowing them to search for them in our Local Data Warehouse using Quick Search algorithm. II. RELATED WORK String-matching is a very significant subject in the wide domain of text processing. Nowadays, this problem received an enormous deal of attention due to various applications in computational biology. String matching algorithms play a key role in most of computer science problems, challenges and in implementation of computer software. String-matching algorithms work as follows [17]: They compare the text with size n with the pattern which size is equal to m. They first put the left ends of the pattern and the text, then compare text characters with pattern characters and after a mismatch among the comparison between the pattern and the text or a whole match between them they shift the pattern to the right and the same procedure is repeated until the the pattern reach to the right end of the text. Our research included a survey of seven Exact String- matching algorithms, which they are Boyer-Moore algorithm Application of Exact String Matching Algorithms towards SMILES Representation of Chemical Structure Ahmad Fadel Klaib, Zurinahni Zainol, Nurul Hashimah Ahamed, Rosma Ahmad, and Wahidah Hussin B World Academy of Science, Engineering and Technology International Journal of Chemical and Molecular Engineering Vol:1, No:10, 2007 83 International Scholarly and Scientific Research & Innovation 1(10) 2007 scholar.waset.org/1307-6892/12146 International Science Index, Chemical and Molecular Engineering Vol:1, No:10, 2007 waset.org/Publication/12146