Abstract

DNA sequence search is a fundamental topic in bioinformatics. The Smith-Waterman algorithm achieved highest accuracy among various sequence alignment tools, but it usually spends much computational time to search on large DNA sequence database. On the contrary, BLAST and FASTA have improved the search speed by using heuristic approaches, by there is a possibility of missing an alignment or giving inaccurate output. This paper presents an efficient hierarchical method to improve the search speed while the accurate is being kept constant. For a given query sequence, firstly, a fast histogram based method is used to scan the sequences in the database. A large number of DNA sequences with low similarity will be excluded for latter searching. The Smith- Waterman algorithm is then applied to each remainder sequences. Experimental results show the proposed method combining histogram information and Smith-Waterman algorithm is a more efficient algorithm for DNA sequence search.

Highlights

  • A FAST SEARCH METHOD FOR DNA SEQUENCE DATABASE USING HISTOGRAM INFORMATIONAbstract- DNA sequence search is a fundamental topic in bioinformatics

  • Comparison of genome sequences (DNA, mRNA and protein) is the most important task in the life science area

  • We present a new search method for DNA sequence matching in a large size

Read more

Summary

A FAST SEARCH METHOD FOR DNA SEQUENCE DATABASE USING HISTOGRAM INFORMATION

Abstract- DNA sequence search is a fundamental topic in bioinformatics. The Smith-Waterman algorithm achieved highest accuracy among various sequence alignment tools, but it usually spends much computational time to search on large DNA sequence database. This paper presents an efficient hierarchical method to improve the search speed while the accurate is being kept constant. For a given query sequence, firstly, a fast histogram based method is used to scan the sequences in the database. A large number of DNA sequences with low similarity will be excluded for latter searching. Experimental results show the proposed method combining histogram information and Smith-Waterman algorithm is a more efficient algorithm for DNA sequence search. Key words - Fast search, DNA sequence, Histogram information, Smith-Waterman algorithm

Introduction
Experiments and Discussions
Findings
Conclusion
Full Text
Published version (Free)

Talk to us

Join us for a 30 min session where you can share your feedback and ask us any queries you have

Schedule a call