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OE Matching Algorithm for Searching Biological Sequences

By Ahmad Klaib and Hugh Osborne

Abstract

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: ISRST
Year: 2009
OAI identifier: oai:eprints.hud.ac.uk:9918

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Citations

  1. (2004). 16). Brute Force Algorithms: Motif Finding [Online]. Available: Fig. 3 average elapsed time (s.) for searching different length of patterns
  2. (2004). 16). Brute Force Algorithms: Motif Finding [Online]. Available: http://ocw.mit.edu/NR/rdonlyres/Mathematics/18-417Fall-2004/8BA 92AB3-A9CD-4719-A4AC1AAFDB8AE5A0/0/lecture_03.pdf
  3. (2008). A Fast Exact Pattern Matching Algorithm for doi
  4. (2008). A Fast Pattern Matching Algorithm for Biological Sequences," doi
  5. (2004). A fast pattern matching algorithm,” doi
  6. (1977). A fast string searching algorithm,” doi
  7. (1990). A very fast substring search algorithm," doi
  8. (2007). Application of Exact String Matching Algorithms towards
  9. BRQS Matching Algorithm for searching Protein Sequence Databases,” unpublished. doi
  10. (2001). Fast string matching algorithm and experimental results,",
  11. (2003). Fast-search: A new efficient variant of the Boyer–Moore string matching algorithm”, doi
  12. (2008). for Bioinformatics (SIB) and the European Bioinformatics Institute (EBI). doi
  13. Handbook of exact string matching Algorithms. doi
  14. (2006). Obtaining the Boyer-Moore String-Matching Algorithm by doi
  15. (1987). On improving the average case of the Boyer-Moore string matching algorithm,”
  16. (1980). Practical fast searching in strings,” doi
  17. (2005). Protein Structure Prediction using Decision Lists,” M.S thesis,
  18. (2008). Searching Protein Sequence Database Using BRBMH Matching Algorithm,” doi
  19. (2008). Searching Similar Antimicrobial Structures Using Quick Search and
  20. (2005). String Matching: Boyer-Moore Algorithm. doi
  21. (2000). The SWISS-PROT protein sequence database and its supplement TrEMBL in doi
  22. (1992). Tuning the Boyer–Moore–Horspool String Searching Algorithm,” doi
  23. (2006). TVSBS: A fast exact pattern matching algorithm for biological sequences,”

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