Fidan Gelişim Algoritması Yardımı ile DNA Motiflerinin Keşfi

Year 2011, Volume: 8 Issue: 1, - , 01.05.2011

Murat Demir Ali Karcı Mehmet Özdemir

Abstract

Motif, a DNA particle, has an important role in the formation of DNA sequences
or in the placement of the regular DNA particles. The discovery of motif is the
operation of finding out the potential DNA particles that are able to transform into motifs
in a given DNA sequence. In this study, with the help of Sapling Growing up Algorithm,
Motif discovery has been realized on the DNA sequences.
Sapling Growing up Algorithm is an algorithm developed as a result of the study concerning
sapling growth. In this method, the data that may be of help in solving the problem are
put into strings of solution that are called “sapling”. Sowing of the saplings, mating, branching, and vaccinating are taken as operators. Sowing of the saplings provides the
formation of new saplings (solutions) in the search space. Branching provides the local
searching, and mating provides the global searching. Vaccinating, however, provides the
exchange of information between similar saplings.
In literature, some of the methods on motif discovery studies are as follows: AlignACE,
MEME, MEME3, MotifSampler, Consensus, Weeder, etc. The results attained in this
study have been compared with AlignACE, MEME, MEME3, MotifSampler, Consensus,
Weeder methods’ results in the conclusion part of the paper. The data in this paper have
been obtained form TRANSFAC database.

Keywords

DNA, motifs of DNA, saplings growing up algorithm

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