MatrixMotif

We propose MatrixMotif(MM), a new combinatorial hybrid algorithm allowing qualitative and quantitative analysis of TFBS (Transcription Factor Binding Site) motifs using NGS data originated from DNA extraction and enrichment techniques. MM allows de novo motifs discovery and motifs iteration employing enumerative and probabilistic models based on several types of matrixes. MM primarily utilizes set of sequences from NGS in fasta format as a template for mathematical and statistical modeling. Fasta format can be generated from fastq format (Illumina platform) set of individual enriched sequences. MM generates final motifs as PPM, PWM or TFFM allowing visualization of de novo computed motifs.