I am trying to annotate a ~300KB region from a insect genome which is a non-protein coding/ cis-regulatory region. I am primarily interested to identify all transcription factor binding sites. I have found lots of web based programs but not sure which one would be best fit for a insect genome?
I have also seen bioconductor packages to carry on transcription factor binding sites. If someone can point out to a comprehensive method to identify TF binding sites in a sequence that would be very helpful.
Thanks in advance for your help.