An easy-to-use webtool for k-mer identification and TFBM association
Introduction
To streamline the identification and visualization of k-mers using our pipeline in an intuitive manner, we built a new webtool, Predictive Regulatory Element Database for Identifying Cis-regulatory elements and Transcription factors webtool (PREDICT), for conducting the motif search using k-mer pipeline, visualizing k-mer sites along genes and associating k-mers to the known TFBMs.Prepare your own gene lists and run the tool online : PREDICT
HOWTO
Users prepare the pre-defined lists of True Positive (i.e., genes with interested expression patterns) and True Negative (i.e., genes without regulatory patterns) based on the expression patterns observed in the dataset. These lists are saved in .txt files prior to uploading. The users have the option to upload the sequence files in tab-delimited format for the genomic regions of genes from the species of their interests, or they may choose to work with the built-in promoter files of all genes (Arabidopsis thaliana, Oryza sativa cv. japonica, etc.)