EMSA - (Sep/30/2007 )
Hi Guys,
I have to start EMSA for my promoter and the transcription factor I am looking at.
The thing is I am really new to it. Can any one please suggest me the best free online programe in which i can feed my predicted promoter sequence to get the transcription factor list.
what similarity number should be appropriate to decide wheather a binding site is present or not in the promoter.
please help me with the informations .
regards
Vani
-vani.khare-
QUOTE (vani.khare @ Oct 1 2007, 04:52 AM)
Hi Guys,
I have to start EMSA for my promoter and the transcription factor I am looking at.
The thing is I am really new to it. Can any one please suggest me the best free online programe in which i can feed my predicted promoter sequence to get the transcription factor list.
what similarity number should be appropriate to decide wheather a binding site is present or not in the promoter.
please help me with the informations .
regards
Vani
I have to start EMSA for my promoter and the transcription factor I am looking at.
The thing is I am really new to it. Can any one please suggest me the best free online programe in which i can feed my predicted promoter sequence to get the transcription factor list.
what similarity number should be appropriate to decide wheather a binding site is present or not in the promoter.
please help me with the informations .
regards
Vani
Try TFSearch it's free and easy to use. Just paste in the promoter and set an organism. A threshold of 85 works OK but you can raise or lower this depending on the number of results. There are other programs around but I haven't really used them.
Ceri
-Ceri-