I was wondering whether anyone has used TFDsearch by Lee Frank Kolakowski?
I am having alot of difficulty with it. According to the instructions,
no particular format is required because it automatically uses ReadSeq to
convert to the appropriate format. When I execute the software, the
results I get seem rather strange...I am able to get transcription factor
sites beyond the length of the nucleotide sequence I submit for analysis
(eg the sequence is only 688 but I get transcription sites at position
700). The sites listed within the actual sequence also do not correspond
with the actual sequence. Not sure why this happens? Does anyone know
the E-mail of the author so that I could contact him as well? Thanks!