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HELEN • 0@ba287559
Last seen 11 weeks ago
Hello, i would like to find the trascription factors in my DNAsequences. These sequences are in FASTA format and they from the mouse. I have this code. But in subject i want to read the sequences from the fasta format with the readFASTA but i don't know how to do it. Thank you very much.
library(TFBSTools) library(JASPAR2020) library(Biostrings) library(S4Vectors) data(MA0003.2) data(MA0004.1) pwmList <- PWMatrixList(MA0003.2=toPWM(MA0003.2), MA0004.1=toPWM(MA0004.1), use.names=TRUE) subject <- DNAString("GAATTCTCTCTTGTTGTAGTCTCTTGACAAAATG") SiteSetList <- searchSeq(pwmList, subject, seqname="seq1", min.score="60%", strand="*") head(writeGFF3(SiteSetList))