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A New String Matching Algorithm for Searching Biological Sequences

By Ahmad Klaib and Hugh Osborne


String matching algorithms play a key role in many\ud computer science problems, and in the implementation of\ud computer software. This problem has received, and\ud continues to receive a great deal of attention due to\ud various applications in text manipulation, information\ud retrieval, speech recognition, image and signal\ud processing and computational biology. In this study, we\ud propose a new algorithm called the Odd and Even\ud algorithm (OE). OE combines an enhanced preprocessing\ud phase from the Berry Ravindran algorithm with our\ud proposed new searching phase procedure. This variety of\ud searching order allows our proposed algorithm to reduce\ud the number of comparison characters and enhances the\ud searching response time. Experimental results show that\ud OE algorithm offers a smaller number of comparisons\ud and offers improved elapsed searching time when\ud compared to other well-known algorithms for searching\ud any length of alphabets and patterns. The proposed\ud algorithm is applicable to searching protein sequence\ud databases as well as any other string searching\ud applications

Topics: Q1, QD
Publisher: ICICS
Year: 2009
OAI identifier:

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  4. (2004). A fast pattern matching algorithm,” doi
  5. (1977). A fast string searching algorithm,” doi
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  7. (2007). Application of Exact String Matching Algorithms towards
  8. BRQS Matching Algorithm for searching Protein Sequence Databases,” unpublished. doi
  9. (2001). Fast string matching algorithm and experimental results,",
  10. (2003). Fast-search: A new efficient variant of the Boyer–Moore string matching algorithm”, doi
  11. (2008). for Bioinformatics (SIB) and the European Bioinformatics Institute (EBI). doi
  12. Handbook of exact string matching Algorithms. doi
  13. (2006). Obtaining the Boyer-Moore String-Matching Algorithm by doi
  14. (1987). On improving the average case of the Boyer-Moore string matching algorithm,”
  15. (1980). Practical fast searching in strings,” doi
  16. (2005). Protein Structure Prediction using Decision Lists,” M.S thesis,
  17. (2008). Searching Protein Sequence Database Using BRBMH Matching Algorithm,” doi
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  19. (2005). String Matching: Boyer-Moore Algorithm. doi
  20. (2000). The SWISS-PROT protein sequence database and its supplement TrEMBL in doi
  21. (1992). Tuning the Boyer–Moore–Horspool String Searching Algorithm,” doi
  22. (2006). TVSBS: A fast exact pattern matching algorithm for biological sequences,”

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