※ Documentation:
Frequently Asked Questions:

1. Q: How to use BDM-PUB server?

A: Firstly, let's go to the prediction page at http://bdmpub.biocuckoo.org/prediction.php. Then input FASTA-format protein primary sequence(s) into the Textbox. You can click on the "Example (human XX protein)" button for an example sequence. After that, choose which cut-off value you want and press the "Submit" button for the final prediction results. Although both raw sequence and FASTA format are permitted, we recommend that users employ the FASTA format.

2. Q: Now I get all the prediction results that I need, but I can't automatically analyze them in my own program.

A: We have provided this functionality for users' convenience! After you get the prediction results, you may click the word here in the sentence "Download the TAB-deliminated data file from here", and get a TAB-deliminated result file which should satisfy the need of automatical processing.

3. Q: There are some "*" characters in predicted peptides. What's their meaning?

A: BDM-PUB has deployed a window with a length of 15aa (a lysine/K residue flanking with 7aa upstream and 7aa downstream). For lysine residues at N- and C-terminal that can not constitute a full 15aa peptide, BDM-PUB use "*" characters as pseudo amino acids to help the prediction.

4. Q: I have a few questions which are not listed above, how can I contact the authors of BDM-PUB?

A: You may contact the corresponding author: Dr. Yu Xue for details.


For publication of results, please cite the following article:

BDM-PUB: Computational Prediction of Protein Ubiquitination Sites with a Bayesian Discriminant Method.
Ao Li, Xinjiao Gao, Jian Ren, Changjiang Jin, and Yu Xue.

Last update: April. 11th, 2009
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