ZIFIBI: Prediction of DNA binding sites for zinc finger proteins.
The cis-regulatory region of target genes is key elements in the transcriptional regulation of gene expression. Many of these cis-regulatory regions have not been identified by either biological experiments or computational methods. Recently, a few additional C(2)H(2) zinc finger transcription factor binding sites have been discovered. The majority of the zinc finger binding sites, however, are still unknown. In this study, we used publically available data to evaluate possible interaction patterns between nucleotides and the amino acids of zinc finger domains. We calculated the most probable state path of three nucleotides sequences using a Hidden Markov Model (HMM). We used these computations to predict C(2)H(2) zinc finger transcription factor binding sites in cis-regulatory regions of their target genes (http://bioinfo.hanyang.ac.kr/ZIFIBI/frameset.php).
Cho
Soo Young
SY
Division of Molecular and Life Sciences, Hanyang University, Sa 3 dong, Ansan, Kyunggodo 425-791, Republic of Korea.
Chung
Myungguen
M
Park
Minyoung
M
Park
Sungjin
S
Lee
Young Seek
YS
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D030541:Databases, Genetic; D006801:Humans; D008954:Models, Biological; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism*; D016335:Zinc Fingers
D014157:Transcription Factors; D004247:DNA