A discrete artificial bee colony algorithm for detecting transcription factor binding sites in DNA sequences

Creative Commons License

KARABOĞA D., Aslan S.

GENETICS AND MOLECULAR RESEARCH, cilt.15, sa.2, 2016 (SCI-Expanded) identifier identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 15 Sayı: 2
  • Basım Tarihi: 2016
  • Doi Numarası: 10.4238/gmr.15028645
  • Dergi Adı: GENETICS AND MOLECULAR RESEARCH
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Anahtar Kelimeler: Bioinformatics, Motif discovery, Binding sites, Artificial bee colony, Discrete optimization
  • Erciyes Üniversitesi Adresli: Evet

Özet

The great majority of biological sequences share significant similarity with other sequences as a result of evolutionary processes, and identifying these sequence similarities is one of the most challenging problems in bioinformatics. In this paper, we present a discrete artificial bee colony (ABC) algorithm, which is inspired by the intelligent foraging behavior of real honey bees, for the detection of highly conserved residue patterns or motifs within sequences. Experimental studies on three different data sets showed that the proposed discrete model, by adhering to the fundamental scheme of the ABC algorithm, produced competitive or better results than other metaheuristic motif discovery techniques.