Transcription factor binding site analysis

Updated 2013 October 4th. Recently I've been looking into transcription factor binding site analyses. With my mind set on this, I thought I'll brush up this old post. MEME is a tool for discovering motifs in a group of related DNA or protein sequences. As a discovery tool, it is able to find de novo...

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Genome scan for 6mer frequency

Split the genome into 6 bp windows and calculate the 6 mer frequencies. Scanning chr6 of hg19: NNNNNN: 3719950 aaaaaa: 373380 tttttt: 372667 TTTTTT: 184768 AAAAAA: 182652 aaaaat: 143055 attttt: 142671 ATTTTT: 133646 TTTAAA: 133284 AAAAAT: 133130 TATTTT: 130672 AAAATA: 129572 TTTTAA: 129570 TTAAAA: 129177 aaaata: 123528 tatttt: 123134 atatat: 119872 ...

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