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Tag Archives: 6mer
Motifs upstream of RefSeq gene models
Here’s a very primitive way of looking for motifs upstream of RefSeq gene models. 1) Download the upstream sequences (-50) of RefSeq gene models using the UCSC Table Browser tool as a bed file 2) Using the fastaFromBed tool from … Continue reading
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: … Continue reading