Earticle

초록

영어

Fast and exact searching for sequences similar to a query sequence in genomic databases remains a challenging task in molecular biology. In this paper, the problem of finding all e-matches in a large genomic database is considered, i.e. all local alignments over a given length w and an error rate of at most e. A new database searching algorithm called QFLA is designed to solve this problem. The proposed algorithm is a full-sensitivity algorithm which is a refined q-gram filter and implemented on a q-gram index. First, new features are extracted from match-regions by logically partitioning both query sequence and genomic database. Second, a large part of irrelevant subsequences are eliminated quickly by these new features during the searching process. Last, the unfiltered regions are verified by the well-known smith-waterman algorithm. The experimental results demonstrate that our algorithm saves time by improving filtration efficiency in a short filtration time.

목차

Abstract
 1. Introduction
 2. Preliminaries
 3. A Refined Q-gram Filter
  3.1. Match-region Feature Extraction Based on Partition
  3.2. New Filter
  3.3. Invalidation and Degeneration
 4. Analysis
 5. Experimental Results
  5.1. Experimental Environment
  5.2. Parameter z
  5.3. Performance
  5.4. Discussion
 6. Conclusion
 References

키워드

저자

• Decai Sun [ College of Information Science and Technology, Bohai University, Jinzhou 121013, China ]
• Xiaoxia Wang [ Teaching and Research Institute of College Computer, Bohai university, Jinzhou 121013, China. ]

참고문헌

발행기관

간행물

표지보기 관심저널 등록

• 간행물명

  International Journal of Hybrid Information Technology

• 간기

  격월간

• pISSN

  1738-9968

• 수록기간

  2008~2016

• 십진분류

  KDC 505 DDC 605