Capstone Project

M.H.S. in Bioinformatics

Jichao Chen


     Ten binding motifs of 14 bp were generated based on an experimentally determined bind consensus (in the form of a frequency distribution for each position) for transcription factor Nr2e3 (see references). Each motif was flanked by 500 random nucleotides to generate 10 input sequences, which was analyzed by "Comtifinder". The results may be obtained on-line here. A visual plot of the distribution of the identified motif is shown below (pdf) with the scores plotted along each of the 10 sequences. Note that 9 out of the 10 sequences have the largest peak in the middle, which is exactly one would expect based on the way the sequences are simulated. The two largest peaks in each sequence are given as the identified common motifs.