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))

You should use readDNAStringSet to read in a FASTA file, as searchSeq expects a DNAStringSet.