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 BEDTools, make fasta files from the bed file 3) Look for motifs Here's the main...

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: 129572 TTTTAA: 129570 TTAAAA: 129177 aaaata: 123528 tatttt: 123134 atatat: 119872 ...

Continue Reading