Performance and analysis of modified voting algorithm for planted motif search

Mostafa Abbas, Hazem M. Bahig

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

Abstract

We consider the planted (l, d) motif search problem, which consists of finding a substring of length l that occurs in a set of input sequences {s 1, s2, ⋯ sn} with maximum Hamming distance, d, around the similar substring. In this paper, we present an experimental comparison between voting algorithm and its modification for planted motif on simulated data from (9, d) to (15, d) in case of challenging instances. The experimental results show that the modified voting algorithm is not better than voting algorithm as theoretically suggested. The results show that the running of voting algorithm is faster than modified voting algorithm in all the cases studied. We also determine, experimentally, the number of sequences that are required to make the modified voting algorithm faster than voting algorithm.

Original languageEnglish
Title of host publication2009 IEEE/ACS International Conference on Computer Systems and Applications, AICCSA 2009
Pages725-731
Number of pages7
DOIs
Publication statusPublished - 19 Oct 2009
Externally publishedYes
Event7th IEEE/ACS International Conference on Computer Systems and Applications, AICCSA-2009 - Rabat, Morocco
Duration: 10 May 200913 May 2009

Other

Other7th IEEE/ACS International Conference on Computer Systems and Applications, AICCSA-2009
CountryMorocco
CityRabat
Period10/5/0913/5/09

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Keywords

  • Bioinformatics
  • Exact algorithms
  • Planted motif search problem
  • Voting technique

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Computer Science Applications
  • Electrical and Electronic Engineering

Cite this

Abbas, M., & Bahig, H. M. (2009). Performance and analysis of modified voting algorithm for planted motif search. In 2009 IEEE/ACS International Conference on Computer Systems and Applications, AICCSA 2009 (pp. 725-731). [5069407] https://doi.org/10.1109/AICCSA.2009.5069407