OTFBS FAQ:

Question 1.The program seems return no results, why?

Answer:

• Well, simply because it can not detect any over-represented binding sites from your sequences.
• OTFBS requires a group of upstream regulatory regions for a set of genes which was assumed to be co-regulated or similarly regulated. If you just submitted one upstream sequence to the program, it will usually return no results. If you are just going to investigate one sequence, you can try the other transcription factor binding sites identification programs. Or you should try to find out the related upstream sequences, which were assumed to be co-regulated or similarly regulated with your sequence. Then summit all these sequences (including your original upstream sequence) to OTFBS. If the sequences were grouped properly, more reliable result will be produced by OTFBS.

Advices:

• Generally the program requires a group of sequences as input, not just one upstream sequence! If you have one upstream region in hand, may be you need to find more related sequences before using OTFBS.
• Submit one group of related upstream sequences at one time. If you have several groups of sequences, do not mix them up, just one group at one time!

Question 2: I want to know the detail of how it works, where to find the reference?

Answer: OTFBS in described in detail in the paper: An approach to identify over-represented cis-elements in related sequences Nucl. Acids. Res. 2003 31: 1995-2005. You can also find it in the publication list.