Extraction of Defensin Antimicrobial Peptide from SWISS-PROT database using Extended Boyer-Moore Algorithm

Abstract

Antimicrobial Peptide (AMP) is a subset of protein that plays an essential role in innate immu nity system. Researches on AMP are actively conducted in Immunology field where synthetics antibiotics are being developed. There are several classifications of AMP’s families with different mechanis m in immobilizing pathogens. Thus, family classification could help speed up a search for specific family AMP. Efforts have been made by active bioinformaticians to build databases to gather AMP data. However, explicit family classification is not featured in these databases due to the method they used for extracting AMP data which is based on literature mining using keywords such as “anticancer”, “antibacterial” and etc. This research aimed to find AMP family’s characteristics and method that enable us to extract AMP data based on its motif. Based on sequence signature resulted from Multiple Sequence Alignment on known antimicrob ial peptide sequences from other research work, we proposed an Extended Boyer-Moore Algorithm (EBMA) as a method of extraction for Defensin AMP data from SWISS-PROT database. We constructed a local data mart specifically to store data extracted by EBMA. The evaluation of this algorithm shows that it i s accurate in extracting Defensin AMP, fast and reliable.